Sequence Homology, Amino Acid
Sequence Homology, Nucleic Acid
Amino Acid Sequence
Molecular Sequence Data
Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.
The arrangement of two or more amino acid or base sequences from an organism or organisms in such a way as to align areas of the sequences sharing common properties. The degree of relatedness or homology between the sequences is predicted computationally or statistically based on weights assigned to the elements aligned between the sequences. This in turn can serve as a potential indicator of the genetic relatedness between the organisms.
Nucleic Acid Hybridization
Widely used technique which exploits the ability of complementary sequences in single-stranded DNAs or RNAs to pair with each other to form a double helix. Hybridization can take place between two complimentary DNA sequences, between a single-stranded DNA and a complementary RNA, or between two RNA sequences. The technique is used to detect and isolate specific sequences, measure homology, or define other characteristics of one or both strands. (Kendrew, Encyclopedia of Molecular Biology, 1994, p503)
A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine).
A species of gram-negative, facultatively anaerobic, rod-shaped bacteria (GRAM-NEGATIVE FACULTATIVELY ANAEROBIC RODS) commonly found in the lower part of the intestine of warm-blooded animals. It is usually nonpathogenic, but some strains are known to produce DIARRHEA and pyogenic infections. Pathogenic strains (virotypes) are classified by their specific pathogenic mechanisms such as toxins (ENTEROTOXIGENIC ESCHERICHIA COLI), etc.
DNA Restriction Enzymes
Enzymes that are part of the restriction-modification systems. They catalyze the endonucleolytic cleavage of DNA sequences which lack the species-specific methylation pattern in the host cell's DNA. Cleavage yields random or specific double-stranded fragments with terminal 5'-phosphates. The function of restriction enzymes is to destroy any foreign DNA that invades the host cell. Most have been studied in bacterial systems, but a few have been found in eukaryotic organisms. They are also used as tools for the systematic dissection and mapping of chromosomes, in the determination of base sequences of DNAs, and have made it possible to splice and recombine genes from one organism into the genome of another. EC 3.21.1.
Structural Homology, Protein
src Homology Domains
Regions of AMINO ACID SEQUENCE similarity in the SRC-FAMILY TYROSINE KINASES that fold into specific functional tertiary structures. The SH1 domain is a CATALYTIC DOMAIN. SH2 and SH3 domains are protein interaction domains. SH2 usually binds PHOSPHOTYROSINE-containing proteins and SH3 interacts with CYTOSKELETAL PROTEINS.
The restriction of a characteristic behavior, anatomical structure or physical system, such as immune response; metabolic response, or gene or gene variant to the members of one species. It refers to that property which differentiates one species from another but it is also used for phylogenetic levels higher or lower than the species.
Sequence Analysis, DNA
Protein Structure, Tertiary
The level of protein structure in which combinations of secondary protein structures (alpha helices, beta sheets, loop regions, and motifs) pack together to form folded shapes called domains. Disulfide bridges between cysteines in two different parts of the polypeptide chain along with other interactions between the chains play a role in the formation and stabilization of tertiary structure. Small proteins usually consist of only one domain but larger proteins may contain a number of domains connected by segments of polypeptide chain which lack regular secondary structure.
RNA sequences that serve as templates for protein synthesis. Bacterial mRNAs are generally primary transcripts in that they do not require post-transcriptional processing. Eukaryotic mRNA is synthesized in the nucleus and must be exported to the cytoplasm for translation. Most eukaryotic mRNAs have a sequence of polyadenylic acid at the 3' end, referred to as the poly(A) tail. The function of this tail is not known for certain, but it may play a role in the export of mature mRNA from the nucleus as well as in helping stabilize some mRNA molecules by retarding their degradation in the cytoplasm.
Open Reading Frames
The characteristic 3-dimensional shape of a protein, including the secondary, supersecondary (motifs), tertiary (domains) and quaternary structure of the peptide chain. PROTEIN STRUCTURE, QUATERNARY describes the conformation assumed by multimeric proteins (aggregates of more than one polypeptide chain).
A set of genes descended by duplication and variation from some ancestral gene. Such genes may be clustered together on the same chromosome or dispersed on different chromosomes. Examples of multigene families include those that encode the hemoglobins, immunoglobulins, histocompatibility antigens, actins, tubulins, keratins, collagens, heat shock proteins, salivary glue proteins, chorion proteins, cuticle proteins, yolk proteins, and phaseolins, as well as histones, ribosomal RNA, and transfer RNA genes. The latter three are examples of reiterated genes, where hundreds of identical genes are present in a tandem array. (King & Stanfield, A Dictionary of Genetics, 4th ed)
Repetitive Sequences, Nucleic Acid
Sequences of DNA or RNA that occur in multiple copies. There are several types: INTERSPERSED REPETITIVE SEQUENCES are copies of transposable elements (DNA TRANSPOSABLE ELEMENTS or RETROELEMENTS) dispersed throughout the genome. TERMINAL REPEAT SEQUENCES flank both ends of another sequence, for example, the long terminal repeats (LTRs) on RETROVIRUSES. Variations may be direct repeats, those occurring in the same direction, or inverted repeats, those opposite to each other in direction. TANDEM REPEAT SEQUENCES are copies which lie adjacent to each other, direct or inverted (INVERTED REPEAT SEQUENCES).
Polymerase Chain Reaction
In vitro method for producing large amounts of specific DNA or RNA fragments of defined length and sequence from small amounts of short oligonucleotide flanking sequences (primers). The essential steps include thermal denaturation of the double-stranded target molecules, annealing of the primers to their complementary sequences, and extension of the annealed primers by enzymatic synthesis with DNA polymerase. The reaction is efficient, specific, and extremely sensitive. Uses for the reaction include disease diagnosis, detection of difficult-to-isolate pathogens, mutation analysis, genetic testing, DNA sequencing, and analyzing evolutionary relationships.
Recombinant Fusion Proteins
Linear POLYPEPTIDES that are synthesized on RIBOSOMES and may be further modified, crosslinked, cleaved, or assembled into complex proteins with several subunits. The specific sequence of AMINO ACIDS determines the shape the polypeptide will take, during PROTEIN FOLDING, and the function of the protein.
Protein Structure, Secondary
Electrophoresis, Polyacrylamide Gel
Nucleic Acid Conformation
Members of the class of compounds composed of AMINO ACIDS joined together by peptide bonds between adjacent amino acids into linear, branched or cyclical structures. OLIGOPEPTIDES are composed of approximately 2-12 amino acids. Polypeptides are composed of approximately 13 or more amino acids. PROTEINS are linear polypeptides that are normally synthesized on RIBOSOMES.
Genetic Complementation Test
Promoter Regions, Genetic
A polynucleotide consisting essentially of chains with a repeating backbone of phosphate and ribose units to which nitrogenous bases are attached. RNA is unique among biological macromolecules in that it can encode genetic information, serve as an abundant structural component of cells, and also possesses catalytic activity. (Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)
Multicellular, eukaryotic life forms of kingdom Plantae (sensu lato), comprising the VIRIDIPLANTAE; RHODOPHYTA; and GLAUCOPHYTA; all of which acquired chloroplasts by direct endosymbiosis of CYANOBACTERIA. They are characterized by a mainly photosynthetic mode of nutrition; essentially unlimited growth at localized regions of cell divisions (MERISTEMS); cellulose within cells providing rigidity; the absence of organs of locomotion; absence of nervous and sensory systems; and an alternation of haploid and diploid generations.
DNA Transposable Elements
Discrete segments of DNA which can excise and reintegrate to another site in the genome. Most are inactive, i.e., have not been found to exist outside the integrated state. DNA transposable elements include bacterial IS (insertion sequence) elements, Tn elements, the maize controlling elements Ac and Ds, Drosophila P, gypsy, and pogo elements, the human Tigger elements and the Tc and mariner elements which are found throughout the animal kingdom.
A theoretical representative nucleotide or amino acid sequence in which each nucleotide or amino acid is the one which occurs most frequently at that site in the different sequences which occur in nature. The phrase also refers to an actual sequence which approximates the theoretical consensus. A known CONSERVED SEQUENCE set is represented by a consensus sequence. Commonly observed supersecondary protein structures (AMINO ACID MOTIFS) are often formed by conserved sequences.
Sequence Analysis, Protein
Gene Expression Regulation
Amino Acid Motifs
CELL LINES derived from the CV-1 cell line by transformation with a replication origin defective mutant of SV40 VIRUS, which codes for wild type large T antigen (ANTIGENS, POLYOMAVIRUS TRANSFORMING). They are used for transfection and cloning. (The CV-1 cell line was derived from the kidney of an adult male African green monkey (CERCOPITHECUS AETHIOPS).)
Synthetic or natural oligonucleotides used in hybridization studies in order to identify and study specific nucleic acid fragments, e.g., DNA segments near or within a specific gene locus or gene. The probe hybridizes with a specific mRNA, if present. Conventional techniques used for testing for the hybridization product include dot blot assays, Southern blot assays, and DNA:RNA hybrid-specific antibody tests. Conventional labels for the probe include the radioisotope labels 32P and 125I and the chemical label biotin.
Saccharomyces cerevisiae Proteins
Family of RNA viruses that infects birds and mammals and encodes the enzyme reverse transcriptase. The family contains seven genera: DELTARETROVIRUS; LENTIVIRUS; RETROVIRUSES TYPE B, MAMMALIAN; ALPHARETROVIRUS; GAMMARETROVIRUS; RETROVIRUSES TYPE D; and SPUMAVIRUS. A key feature of retrovirus biology is the synthesis of a DNA copy of the genome which is integrated into cellular DNA. After integration it is sometimes not expressed but maintained in a latent state (PROVIRUSES).
A set of three nucleotides in a protein coding sequence that specifies individual amino acids or a termination signal (CODON, TERMINATOR). Most codons are universal, but some organisms do not produce the transfer RNAs (RNA, TRANSFER) complementary to all codons. These codons are referred to as unassigned codons (CODONS, NONSENSE).
Chromatography, High Pressure Liquid
Accumulation of a drug or chemical substance in various organs (including those not relevant to its pharmacologic or therapeutic action). This distribution depends on the blood flow or perfusion rate of the organ, the ability of the drug to penetrate organ membranes, tissue specificity, protein binding. The distribution is usually expressed as tissue to plasma ratios.
The most abundant form of RNA. Together with proteins, it forms the ribosomes, playing a structural role and also a role in ribosomal binding of mRNA and tRNAs. Individual chains are conventionally designated by their sedimentation coefficients. In eukaryotes, four large chains exist, synthesized in the nucleolus and constituting about 50% of the ribosome. (Dorland, 28th ed)
Gene Expression Regulation, Bacterial
The intracellular transfer of information (biological activation/inhibition) through a signal pathway. In each signal transduction system, an activation/inhibition signal from a biologically active molecule (hormone, neurotransmitter) is mediated via the coupling of a receptor/enzyme to a second messenger system or to an ion channel. Signal transduction plays an important role in activating cellular functions, cell differentiation, and cell proliferation. Examples of signal transduction systems are the GAMMA-AMINOBUTYRIC ACID-postsynaptic receptor-calcium ion channel system, the receptor-mediated T-cell activation pathway, and the receptor-mediated activation of phospholipases. Those coupled to membrane depolarization or intracellular release of calcium include the receptor-mediated activation of cytotoxic functions in granulocytes and the synaptic potentiation of protein kinase activation. Some signal transduction pathways may be part of larger signal transduction pathways; for example, protein kinase activation is part of the platelet activation signal pathway.
Mutagenesis where the mutation is caused by the introduction of foreign DNA sequences into a gene or extragenic sequence. This may occur spontaneously in vivo or be experimentally induced in vivo or in vitro. Proviral DNA insertions into or adjacent to a cellular proto-oncogene can interrupt GENETIC TRANSLATION of the coding sequences or interfere with recognition of regulatory elements and cause unregulated expression of the proto-oncogene resulting in tumor formation.
A field of biology concerned with the development of techniques for the collection and manipulation of biological data, and the use of such data to make biological discoveries or predictions. This field encompasses all computational methods and theories for solving biological problems including manipulation of models and datasets.
Adaptor Proteins, Signal Transducing
A broad category of carrier proteins that play a role in SIGNAL TRANSDUCTION. They generally contain several modular domains, each of which having its own binding activity, and act by forming complexes with other intracellular-signaling molecules. Signal-transducing adaptor proteins lack enzyme activity, however their activity can be modulated by other signal-transducing enzymes
A molecule that binds to another molecule, used especially to refer to a small molecule that binds specifically to a larger molecule, e.g., an antigen binding to an antibody, a hormone or neurotransmitter binding to a receptor, or a substrate or allosteric effector binding to an enzyme. Ligands are also molecules that donate or accept a pair of electrons to form a coordinate covalent bond with the central metal atom of a coordination complex. (From Dorland, 27th ed)
Any of various animals that constitute the family Suidae and comprise stout-bodied, short-legged omnivorous mammals with thick skin, usually covered with coarse bristles, a rather long mobile snout, and small tail. Included are the genera Babyrousa, Phacochoerus (wart hogs), and Sus, the latter containing the domestic pig (see SUS SCROFA).
Nucleic Acid Renaturation
Tumor Cells, Cultured
Protein Sorting Signals
Analysis of PEPTIDES that are generated from the digestion or fragmentation of a protein or mixture of PROTEINS, by ELECTROPHORESIS; CHROMATOGRAPHY; or MASS SPECTROMETRY. The resulting peptide fingerprints are analyzed for a variety of purposes including the identification of the proteins in a sample, GENETIC POLYMORPHISMS, patterns of gene expression, and patterns diagnostic for diseases.
Within a eukaryotic cell, a membrane-limited body which contains chromosomes and one or more nucleoli (CELL NUCLEOLUS). The nuclear membrane consists of a double unit-type membrane which is perforated by a number of pores; the outermost membrane is continuous with the ENDOPLASMIC RETICULUM. A cell may contain more than one nucleus. (From Singleton & Sainsbury, Dictionary of Microbiology and Molecular Biology, 2d ed)
Bacterial Outer Membrane Proteins
Species- or subspecies-specific DNA (including COMPLEMENTARY DNA; conserved genes, whole chromosomes, or whole genomes) used in hybridization studies in order to identify microorganisms, to measure DNA-DNA homologies, to group subspecies, etc. The DNA probe hybridizes with a specific mRNA, if present. Conventional techniques used for testing for the hybridization product include dot blot assays, Southern blot assays, and DNA:RNA hybrid-specific antibody tests. Conventional labels for the DNA probe include the radioisotope labels 32P and 125I and the chemical label biotin. The use of DNA probes provides a specific, sensitive, rapid, and inexpensive replacement for cell culture techniques for diagnosing infections.
The large family of plants characterized by pods. Some are edible and some cause LATHYRISM or FAVISM and other forms of poisoning. Other species yield useful materials like gums from ACACIA and various LECTINS like PHYTOHEMAGGLUTININS from PHASEOLUS. Many of them harbor NITROGEN FIXATION bacteria on their roots. Many but not all species of "beans" belong to this family.
Reverse Transcriptase Polymerase Chain Reaction
Expressed Sequence Tags
Cell lines whose original growing procedure consisted being transferred (T) every 3 days and plated at 300,000 cells per plate (J Cell Biol 17:299-313, 1963). Lines have been developed using several different strains of mice. Tissues are usually fibroblasts derived from mouse embryos but other types and sources have been developed as well. The 3T3 lines are valuable in vitro host systems for oncogenic virus transformation studies, since 3T3 cells possess a high sensitivity to CONTACT INHIBITION.
In Situ Hybridization
Proteins that share the common characteristic of binding to carbohydrates. Some ANTIBODIES and carbohydrate-metabolizing proteins (ENZYMES) also bind to carbohydrates, however they are not considered lectins. PLANT LECTINS are carbohydrate-binding proteins that have been primarily identified by their hemagglutinating activity (HEMAGGLUTININS). However, a variety of lectins occur in animal species where they serve diverse array of functions through specific carbohydrate recognition.
The class of all enzymes catalyzing oxidoreduction reactions. The substrate that is oxidized is regarded as a hydrogen donor. The systematic name is based on donor:acceptor oxidoreductase. The recommended name will be dehydrogenase, wherever this is possible; as an alternative, reductase can be used. Oxidase is only used in cases where O2 is the acceptor. (Enzyme Nomenclature, 1992, p9)
Deoxyribonucleases, Type II Site-Specific
Enzyme systems containing a single subunit and requiring only magnesium for endonucleolytic activity. The corresponding modification methylases are separate enzymes. The systems recognize specific short DNA sequences and cleave either within, or at a short specific distance from, the recognition sequence to give specific double-stranded fragments with terminal 5'-phosphates. Enzymes from different microorganisms with the same specificity are called isoschizomers. EC 220.127.116.11.
Epididymal Secretory Proteins
Receptors, Cell Surface
Cell surface proteins that bind signalling molecules external to the cell with high affinity and convert this extracellular event into one or more intracellular signals that alter the behavior of the target cell (From Alberts, Molecular Biology of the Cell, 2nd ed, pp693-5). Cell surface receptors, unlike enzymes, do not chemically alter their ligands.
Amino Acid Substitution
The naturally occurring or experimentally induced replacement of one or more AMINO ACIDS in a protein with another. If a functionally equivalent amino acid is substituted, the protein may retain wild-type activity. Substitution may also diminish, enhance, or eliminate protein function. Experimentally induced substitution is often used to study enzyme activities and binding site properties.
Characterization of an amphioxus paired box gene, AmphiPax2/5/8: developmental expression patterns in optic support cells, nephridium, thyroid-like structures and pharyngeal gill slits, but not in the midbrain-hindbrain boundary region. (1/2913)On the basis of developmental gene expression, the vertebrate central nervous system comprises: a forebrain plus anterior midbrain, a midbrain-hindbrain boundary region (MHB) having organizer properties, and a rhombospinal domain. The vertebrate MHB is characterized by position, by organizer properties and by being the early site of action of Wnt1 and engrailed genes, and of genes of the Pax2/5/8 subfamily. Wada and others (Wada, H., Saiga, H., Satoh, N. and Holland, P. W. H. (1998) Development 125, 1113-1122) suggested that ascidian tunicates have a vertebrate-like MHB on the basis of ascidian Pax258 expression there. In another invertebrate chordate, amphioxus, comparable gene expression evidence for a vertebrate-like MHB is lacking. We, therefore, isolated and characterized AmphiPax2/5/8, the sole member of this subfamily in amphioxus. AmphiPax2/5/8 is initially expressed well back in the rhombospinal domain and not where a MHB would be expected. In contrast, most of the other expression domains of AmphiPax2/5/8 correspond to expression domains of vertebrate Pax2, Pax5 and Pax8 in structures that are probably homologous - support cells of the eye, nephridium, thyroid-like structures and pharyngeal gill slits; although AmphiPax2/5/8 is not transcribed in any structures that could be interpreted as homologues of vertebrate otic placodes or otic vesicles. In sum, the developmental expression of AmphiPax2/5/8 indicates that the amphioxus central nervous system lacks a MHB resembling the vertebrate isthmic region. Additional gene expression data for the developing ascidian and amphioxus nervous systems would help determine whether a MHB is a basal chordate character secondarily lost in amphioxus. The alternative is that the MHB is a vertebrate innovation. (+info)
Conserved domains and lack of evidence for polyglutamine length polymorphism in the chicken homolog of the Machado-Joseph disease gene product ataxin-3. (2/2913)Ataxin-3 is a protein of unknown function which is mutated in Machado-Joseph disease by expansion of a genetically unstable CAG repeat encoding polyglutamine. By analysis of chicken ataxin-3 we were able to identify four conserved domains of the protein and detected widespread expression in chicken tissues. In the first such analysis in a non-primate species we found that in contrast to primates, the chicken CAG repeat is short and genetically stable. (+info)
Sequence analysis and expression of a mouse homolog of human IkappaBL gene. (3/2913)The family of transcriptional inhibitors, IkappaBLs, are critical to the regulation of cytokine and chemokine production. We have identified the complete cDNA sequence of the mouse IkappabL gene. The predicted 381-amino-acid sequence showed evidence of two ankyrin repeats characteristic of Ikappab family proteins and 92% identity to the IkappaBL human homolog. Although human IkappaBL has been reported to be ubiquitously expressed, here we show that mouse IkappaBL is transcribed in a more tissue-specific manner. (+info)
Canine preprorelaxin: nucleic acid sequence and localization within the canine placenta. (4/2913)Employing uteroplacental tissue at Day 35 of gestation, we determined the nucleic acid sequence of canine preprorelaxin using reverse transcription- and rapid amplification of cDNA ends-polymerase chain reaction. Canine preprorelaxin cDNA consisted of 534 base pairs encoding a protein of 177 amino acids with a signal peptide of 25 amino acids (aa), a B domain of 35 aa, a C domain of 93 aa, and an A domain of 24 aa. The putative receptor binding region in the N'-terminal part of the canine relaxin B domain GRDYVR contained two substitutions from the classical motif (E-->D and L-->Y). Canine preprorelaxin shared highest homology with porcine and equine preprorelaxin. Northern analysis revealed a 1-kilobase transcript present in total RNA of canine uteroplacental tissue but not of kidney tissue. Uteroplacental tissue from two bitches each at Days 30 and 35 of gestation were studied by in situ hybridization to localize relaxin mRNA. Immunohistochemistry for relaxin, cytokeratin, vimentin, and von Willebrand factor was performed on uteroplacental tissue at Day 30 of gestation. The basal cell layer at the core of the chorionic villi was devoid of relaxin mRNA and immunoreactive relaxin or vimentin but was immunopositive for cytokeratin and identified as cytotrophoblast cells. The cell layer surrounding the chorionic villi displayed specific hybridization signals for relaxin mRNA and immunoreactivity for relaxin and cytokeratin but not for vimentin, and was identified as syncytiotrophoblast. Those areas of the chorioallantoic tissue with most intense relaxin immunoreactivity were highly vascularized as demonstrated by immunoreactive von Willebrand factor expressed on vascular endothelium. The uterine glands and nonplacental uterine areas of the canine zonary girdle placenta were devoid of relaxin mRNA and relaxin. We conclude that the syncytiotrophoblast is the source of relaxin in the canine placenta. (+info)
Cloning, sequencing, and localization of bovine estrogen receptor-beta within the ovarian follicle. (5/2913)The potential role of estrogen receptor-beta (ERbeta) in normal ovarian folliculogenesis and in reproductive disorders such as ovarian follicular cysts has not been well defined. Therefore, we were interested in cloning, sequencing, and localizing ERbeta mRNA and protein within the bovine ovary. Bovine ERbeta (bERbeta) was amplified by reverse transcription-polymerase chain reaction (RT-PCR), then cloned and sequenced. Results showed that the open reading frame of bERbeta cDNA spanned 1584 nucleotides encoding a protein of 527 amino acids. The N-terminal region of bERbeta was found to be 80% homologous to human and mouse ERbeta and 79% homologous to rat ERbeta. Bovine ERbeta DNA-binding domain was 100% homologous to human, mouse, and rat ERbeta sequences. The C-terminal/ligand-binding domain of bERbeta was 89% homologous to human, 86% homologous to mouse, and 88% homologous to rat ERbeta. Human and bovine ERbeta amino acid sequences are similar in that their coding region extended farther 5' than initially reported for the published rat ERbeta sequence. Using in situ hybridization and immunohistochemistry, ERbeta mRNA and protein, respectively, were demonstrated to be present in granulosa cells of antral follicles in various stages of follicular growth. These findings suggest a role for bERbeta in ovarian follicular growth and maturation. (+info)
X inactive-specific transcript (Xist) expression and X chromosome inactivation in the preattachment bovine embryo. (6/2913)Expression of the X inactive-specific transcript (Xist) is thought to be essential for the initiation of X chromosome inactivation and dosage compensation during female embryo development. In the present study, we analyzed the patterns of Xist transcription and the onset of X chromosome inactivation in bovine preattachment embryos. Reverse transcription-polymerase chain reaction (RT-PCR) revealed the presence of Xist transcripts in all adult female somatic tissues evaluated. In contrast, among the male tissues examined, Xist expression was detected only in testis. No evidence for Xist transcription was observed after a single round of RT-PCR from pools of in vitro-derived embryos at the 2- to 4-cell stage. Xist transcripts were detected as a faint amplicon at the 8-cell stage initially, and consistently thereafter in all stages examined up to and including the expanded blastocyst stage. Xist transcripts, however, were subsequently detected from the 2-cell stage onward after nested RT-PCR. Preferential [3H]thymidine labeling indicative of late replication of one of the X chromosomes was noted in female embryos of different developmental ages as follows: 2 of 7 (28.5%) early blastocysts, 6 of 13 (46.1%) blastocysts, 8 of 11 (72.1%) expanded blastocysts, and 14 of 17 (77.7%) hatched blastocysts. These results suggest that Xist expression precedes the onset of late replication in the bovine embryo, in a pattern compatible with a possible role of bovine Xist in the initiation of X chromosome inactivation. (+info)
Pre-mRNA splicing of IgM exons M1 and M2 is directed by a juxtaposed splicing enhancer and inhibitor. (7/2913)Splicing of certain pre-mRNA introns is dependent on an enhancer element, which is typically purine-rich. It is generally thought that enhancers increase the use of suboptimal splicing signals, and one specific proposal is that enhancers stabilize binding of U2AF65 to weak polypyrimidine (Py) tracts. Here, we test this model using an IgM pre-mRNA substrate, which contains a well-characterized enhancer. Although the enhancer was required for in vitro splicing, we found it had no effect on U2AF65 binding. Unexpectedly, replacement of the natural IgM Py tract, branchpoint, and 5' splice site with consensus splicing signals did not circumvent the enhancer requirement. These observations led us to identify a novel regulatory element within the IgM M2 exon that acts as a splicing inhibitor; removal of the inhibitor enabled splicing to occur in the absence of the enhancer. The IgM M2 splicing inhibitor is evolutionarily conserved, can inhibit the activity of an unrelated, constitutively spliced pre-mRNA, and acts by repressing splicing complex assembly. Interestingly, the inhibitor itself forms an ATP-dependent complex that contains U2 snRNP. We conclude that splicing of IgM exons M1 and M2 is directed by two juxtaposed regulatory elements-an enhancer and an inhibitor-and that a primary function of the enhancer is to counteract the inhibitor. (+info)
Metabolic engineering of poly(3-hydroxyalkanoates): from DNA to plastic. (8/2913)Poly(3-hydroxyalkanoates) (PHAs) are a class of microbially produced polyesters that have potential applications as conventional plastics, specifically thermoplastic elastomers. A wealth of biological diversity in PHA formation exists, with at least 100 different PHA constituents and at least five different dedicated PHA biosynthetic pathways. This diversity, in combination with classical microbial physiology and modern molecular biology, has now opened up this area for genetic and metabolic engineering to develop optimal PHA-producing organisms. Commercial processes for PHA production were initially developed by W. R. Grace in the 1960s and later developed by Imperial Chemical Industries, Ltd., in the United Kingdom in the 1970s and 1980s. Since the early 1990s, Metabolix Inc. and Monsanto have been the driving forces behind the commercial exploitation of PHA polymers in the United States. The gram-negative bacterium Ralstonia eutropha, formerly known as Alcaligenes eutrophus, has generally been used as the production organism of choice, and intracellular accumulation of PHA of over 90% of the cell dry weight have been reported. The advent of molecular biological techniques and a developing environmental awareness initiated a renewed scientific interest in PHAs, and the biosynthetic machinery for PHA metabolism has been studied in great detail over the last two decades. Because the structure and monomeric composition of PHAs determine the applications for each type of polymer, a variety of polymers have been synthesized by cofeeding of various substrates or by metabolic engineering of the production organism. Classical microbiology and modern molecular bacterial physiology have been brought together to decipher the intricacies of PHA metabolism both for production purposes and for the unraveling of the natural role of PHAs. This review provides an overview of the different PHA biosynthetic systems and their genetic background, followed by a detailed summation of how this natural diversity is being used to develop commercially attractive, recombinant processes for the large-scale production of PHAs. (+info)
i used nuva ring the first two days and had unprotcted sex those first two days...ended up removing it and started my...
Ii. Was. On the nuva ring for two daysthe first two days. I had. Unprotected sex decided. That. I. Do want to become. Pregnant so I removed it two. Days later....two days after that I. Started.
Blog - Katanne Belisle RHN
As a busy, do-too-much, everyone-else-comes-first type of person, I learned the hard way that this kind of stress compromises both gut and health. It took ten years to perfect a healing approach that is less about food and more about how we manage our stress.... stress that impacts our digestion, and stress that we over-doers tend to bring on ourselves. We all need efficient and effective solutions that we can integrate today, so here are some simple tips of what to eat and do to bring enjoyment back to your eating and living!. ...
Cloning and characterization of a mouse brain calcitonin receptor complementary deoxyribonucleic acid and mapping of the...
Fingerprint Dive into the research topics of Cloning and characterization of a mouse brain calcitonin receptor complementary deoxyribonucleic acid and mapping of the calcitonin receptor gene. Together they form a unique fingerprint. ...
Tiab1 - Kunitz trypsin inhibitor - Glycine soja (Wild soybean) - Tiab1 gene & protein
p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.,/p> ,p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.,/p> ,p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).,/p> ,p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x,sup>64,/sup> + x,sup>4,/sup> + x,sup>3,/sup> + x + 1. The algorithm is described in the ISO 3309 standard. ,/p> ,p class=publication>Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.,br /> ,strong>Cyclic redundancy and other checksums,/strong>,br /> ,a href=http://www.nrbook.com/b/bookcpdf.php>Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993),/a>),/p> Checksum:i ...
SACOL RS12510 - AureoWiki
Signal transductionRegulatory functionsDNA interactionstranscriptional regulator, Acidobacterial, PadR-family (TIGR03433; HMM-score: 14.4) ...
Anti-mucus tea - Marina Silverio RHN
This material is exclusive to annual members of NutritionPro Mentor. If you are a member, please log in using the Log in tab in the top menu bar.. If you run into problems, please contact nutrition[at]marinarhn.ca.. Thank you.. ...
New Credit Rating: NuVasive
We are initiating our issuer credit rating for NuVasive NUVA at BBB-, reflecting its improving competitive position and cash flow trends. NuVasives Maximum
Gain of OGP, an Estrogen-Regulated Oviduct-Specific Glycoprotein, Is Associated with the Development of Endometrial Hyperplasia...
Oviduct-specific glycoprotein is a glycoprotein secreted by secretory epithelial cells of the oviduct (3) ; recently, we showed that it is ectopically expressed in ovarian cancer (9) . On the basis of the present study of normal, hyperplastic, and malignant endometrial tissues, it appears that a gain of oviduct-specific glycoprotein begins under conditions of unopposed estrogen exposure, which is a known risk factor for the development of endometrioid carcinoma.. Although oviduct-specific glycoprotein is not normally a secretory product of the normal endometrium, we observed focal staining of the stem cells in the basalis layer with some staining in adjacent glands in the functionalis layer (1) . The epithelial cells in the functionalis layer shed each month and regenerate during the next menstrual cycle through proliferation of epithelial cells in the intact basalis layer. It has been proposed that genetic alterations that induce endometrial cancer are acquired sequentially by the nonshedding ...
Molecular evolution of a small gene family of wound inducible Kunitz trypsin inhibitors in Populus. - PubMed - NCBI
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Prevalence, Types, and RNA Concentrations of Human Parechoviruses, Including a Sixth Parechovirus Type, in Stool Samples from...
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I had spotting on my period while on the nuva ring.. Does this mean Im pregnant?
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Gentle Masking of Low-Complexity Sequences Improves Homology Search
Detection of sequences that are homologous, i.e. descended from a common ancestor, is a fundamental task in computational biology. This task is confounded by low-complexity tracts (such as atatatatatat), which arise frequently and independently, causing strong similarities that are not homologies. There has been much research on identifying low-complexity tracts, but little research on how to treat them during homology search. We propose to find homologies by aligning sequences with
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A review of the literature on homology indicates that the theory does not provide evidence for evolutionary naturalism, and that the common examples of homology can be better explained by Creation.
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Novel patterns of gene expression in pituitary adenomas identified by complementary deoxyribonucleic acid microarrays and...
TY - JOUR. T1 - Novel patterns of gene expression in pituitary adenomas identified by complementary deoxyribonucleic acid microarrays and quantitative reverse transcription-polymerase chain reaction. AU - Evans, Chheng Orn. AU - Young, Andrew N.. AU - Brown, Milton R.. AU - Brat, Daniel J.. AU - Parks, John S.. AU - Neish, Andrew S.. AU - Oyesiku, Nelson M.. PY - 2001. Y1 - 2001. N2 - Pituitary adenomas account for approximately 10% of intracranial tumors, but little is known of the oncogenesis of these tumors. The identification of tumor-specific genes may further elucidate the pathways of tumor formation. We used complementary DNA microarrays to examine gene expression profiles in nonfunctioning, PRL, GH, and ACTH secreting adenomas, compared with normal pituitary. Microarray analysis showed that 128 of 7075 genes examined were differentially expressed. We then analyzed three genes with unique expression patterns and oncogenic importance by RT-real time quantitative PCR in 37 pituitaries. ...
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Dissecting the role of low-complexity regions in the evolution of vertebrate proteins.
Low-complexity regions (LCRs) in proteins are tracts that are highly enriched in one or a few amino acids. Given their high abundance, and their capacity to expand in relatively short periods of time through replication slippage, they can greatly con
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Tissue expression of CTTNBP2 - Staining in kidney - The Human Protein Atlas
Expression of CTTNBP2 (C7orf8, CORTBP2, KIAA1758, Orf4) in kidney tissue. Antibody staining with HPA044654 and CAB009151 in immunohistochemistry.
Tissue expression of CTTNBP2 - Staining in stomach 1 - The Human Protein Atlas
Expression of CTTNBP2 (C7orf8, CORTBP2, KIAA1758, Orf4) in stomach 1 tissue. Antibody staining with HPA044654 and CAB009151 in immunohistochemistry.
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... is the biological homology between DNA, RNA, or protein sequences, defined in terms of shared ancestry in the ... "quantify the homology." Based on the definition of homology specified above this terminology is incorrect since sequence ... Partial homology can occur where a segment of the compared sequences has a shared origin, while the rest does not. Such partial ... The term "percent homology" is often used to mean "sequence similarity." The percentage of identical residues (percent identity ...
Machesky LM, Insall RH, Volkman LE (2001). "WASP homology sequences in baculoviruses". Trends Cell Biol. 11 (7): 286-287. doi: ... The WH2 (WASP-Homology 2, or Wiskott-Aldrich homology 2) domain is an ~18 amino acids actin-binding motif. This domain was ... The WH2 motif or WH2 domain is an evolutionarily conserved sequence motif contained in proteins. It is found in WASP proteins ... The WH2 motif (for Wiskott-Aldrich syndrome homology region 2) has been shown in WAS and Scar1/WASF1 (mammalian homologue) to ...
Arthur Everett Pitcher
Exact homomorphism sequences in homology theory "marks the first appearance in print of the term "exact sequence", now ... "Exact homomorphism sequences in homology theory". Ann. Math. 48 (3): 682-709. doi:10.2307/1969135. JSTOR 1969135. Steven H. ... known for early pioneering work on exact sequences and applying Morse theory to homotopy theory. Everett Pitcher grew up in ...
See Homology of sequences in genetics). It is important (but often difficult) to differentiate between paralogs and orthologs ... Resulting sequence usually lack introns and often contain poly, sequences that are also integrated into the genome. Many ... Paralogs can be identified in single genomes through a sequence comparison of all annotated gene models to one another. Such a ... However, many duplications are, in fact, not detrimental or beneficial, and these neutral sequences may be lost or may spread ...
Sequence homology with mucus proteinase inhibitor". Biol. Chem. Hoppe-Seyler. 372 (1): 13-21. doi:10.1515/bchm3.1991.372.1.13. ... Evidence of sequence homology and immunological cross-reactivity". Biol. Chem. Hoppe-Seyler. 373 (1): 27-33. doi:10.1515/ ... Purification, cDNA sequence, and evidence for transglutaminase cross-linking". J. Biol. Chem. 268 (16): 12028-32. PMID 7685029 ... 1992). "Primary structure of the human elafin precursor preproelafin deduced from the nucleotide sequence of its gene and the ...
Complete amino acid sequence as revealed by protein and cDNA sequencing and structural homology to whey proteins and Red Sea ... Sequence homology with mucus proteinase inhibitor". Biological Chemistry Hoppe-Seyler. 372 (1): 13-21. doi:10.1515/bchm3.1991. ... Stetler G, Brewer MT, Thompson RC (Oct 1986). "Isolation and sequence of a human gene encoding a potent inhibitor of leukocyte ... Thompson RC, Ohlsson K (Sep 1986). "Isolation, properties, and complete amino acid sequence of human secretory leukocyte ...
They display significant amino acid sequence homology. Sixteen cysteine residues, forming 8 disulfide bonds, are strictly ... A sequence comparison of piscivorin and other CRISP family proteins suggests that the Glu186 residue is the crucial site for ... The nucleotide sequence of piscivorin cDNA spans 1323 bp, containing an open reading frame of 240 codons. Piscivorin has the ... following amino acid sequence. Piscivorin reduces high potassium-evoked smooth muscle contraction, but does not inhibit ...
Endicott, Patrick C; Smith, J Wolfgang (1980). "A homology spectral sequence for submersions" (PDF). Pacific Journal of ... Smith, J (1980). "Fiber homology and orientability of maps" (PDF). Pacific Journal of Mathematics. 89 (2): 453-70. doi:10.2140/ ... Smith, J. Wolfgang (1968). "An exact sequence for submersions" (PDF). Bulletin of the American Mathematical Society. 74 (2): ...
TANK-binding kinase 1
TBK1 is a non-canonical IKK kinase that phosphorylates the nuclear factor kB (NFkB). It shares sequence homology with canonical ...
Innexins have no significant sequence homology with connexins. Though differing in sequence to connexins, innexins are ... C. elegans Sequencing, Consortium (Dec 11, 1998). "Genome sequence of the nematode C. elegans: a platform for investigating ... based on gene mapping and sequence similarity: A, B and C (for example, GJA1, GJC1). However, connexin genes do not ... with an amino acid sequence similar to innexins), in fact functions as a single-membrane channel that communicates with the ...
The sequence homology definition breaks down and comes up with some very unsatisfying answers. Monoploids are no problem with ... If you use the linear sequence homology defintion, then no.. *The cytological defintion states that X and Y are homologous. ... Good luck trying to make sense out of the sequence homology defintion. ... This definition is in parallel with sequence homology. This would exclude nearly all of the X as homologous with Y (all but the ...
... sequence homology with maurotoxin (MTX; α-KTx6.2). Most short-chain scorpion toxins contain three disulfide bridges, whereas ...
Topological data analysis
Persistent homology is closely related to spectral sequences. In particular the algorithm bringing a filtered complex to its ... The main tool is persistent homology, an adaptation of homology to point cloud data. Persistent homology has been applied to ... calculate persistent homology for both datasets unif.phom <- calculate_homology(unif2d) circ.phom <- calculate_homology( ... Taking the homology of each complex in this filtration gives a persistence module H i ( X r 0 ) → H i ( X r 1 ) → H i ( X r 2 ...
Casein kinase 1 isoform epsilon
However its gene sequence shows no sequence homology. In addition, casein kinase 1 epsilon does not completely rescue circadian ... Like dbt, shaggy is not a sequence homolog to casein kinase 1 epsilon. Conversely, Gsk3 is also found in mammals, and mutants ... In this manner, temporally sequenced phosphorylations of PER2 act to delay its degradation rate and may provide insight into ... "A noncanonical sequence phosphorylated by casein kinase 1 in beta-catenin may play a role in casein kinase 1 targeting of ...
Moreover, they share sequence homology with other viroids. Conditions for a viroid to infect its host include wounds on the ... This viroid has 64% sequence homology with the cadang-cadang viroid. There are other related viroids with the CCCVd, which are ... Tinangaja disease is caused by coconut trinangaja viroid (CTiVd), which has 64% sequence homology with CCCVd. This disease has ... CCCVd have a sequence of 246 nucleotides, 44 of which are common with most viroids. CCCVd can add a cytosine residue in the 197 ...
Sequence alignments of the gene cluster and previously functionally characterized glycyl radical enzymes as well as homology ... sequence alignments, homology modeling, and DNA annotation. A key accomplishment of the Balskus lab was the elucidation of the ... a sequence similarity network (SSN) is constructed to group together sequences of enzymes in clusters that share biological ... First an enzyme family of interest is identified (in this case, the GRE family) and the amino acid sequences of all the members ...
Plasminogen activator inhibitor-2
Sequence, chromosomal assignment, and homology to plasminogen activator-inhibitor". The Journal of Experimental Medicine. 166 ( ... Belin D, Guzman LM, Bost S, Konakova M, Silva F, Beckwith J (January 2004). "Functional activity of eukaryotic signal sequences ... as various mutations to the signal sequence can significantly enhance secretion efficiency. PAI-2 is undetectable in adult ... spanning amino acids 379-383 and an N-terminal hydrophobic signal sequence. ...
Viruses can encode proteins with sequence homology to cyclins. One much-studied example is K-cyclin (or v-cyclin) from Kaposi ... The consensus sequence for the phosphorylation site in the amino acid sequence of a CDK substrate is [S/T*]PX[K/R], where S/T* ... Although they lack cyclin sequence homology, crystal structures show that p35 folds in a similar way as the cyclins. However, ... Proteins with no homology to the cyclin family can be direct activators of CDKs. One family of such activators is the RINGO/ ...
Octapeptide sharing sequence homology with HIV envelope protein gp120. It may be useful as antiviral agent in AIDS therapy. The ... core pentapeptide sequence, TTNYT, consisting of amino acids 4-8 in peptide T, is the HIV envelope sequence required for ...
Marcus F, Gontero B, Harrsch PB, Rittenhouse J (Mar 1986). "Amino acid sequence homology among fructose-1,6-bisphosphatases". ... Fructose bisphosphatase deficiency Fructose Gluconeogenesis Metabolism Marcus F, Harrsch PB (May 1990). "Amino acid sequence of ... IMPase and FBPase share a sequence motif (Asp-Pro-Ile/Leu-Asp-Gly/Ser-Thr/Ser) which has been shown to bind metal ions and ... do not show any significant sequence similarity to the enzymes from other organisms. The Bacillus subtilis enzyme is inhibited ...
It shares significant sequence homology with biglycan and decorin. Fibromodulin participates in the assembly of the collagen ... "Entrez Gene: FMOD fibromodulin". Antonsson P, Heinegård D, Oldberg A (1993). "Structure and deduced amino acid sequence of the ... to chromosome 1q32 and completion of the cDNA sequence". Genomics. 23 (3): 715-7. doi:10.1006/geno.1994.1567. PMID 7851907. " ...
"Intermediate sequences increase the detection of homology between sequences". Journal of Molecular Biology. 273 (1): 349-54. ... SCOP sequence searches, alignments and genome assignments". Nucleic Acids Research. 30 (1): 268-272. doi:10.1093/nar/30.1.268. ... With Julian Gough he created the Superfamily database which uses Hidden Markov models to identify protein sequences that are ... His certificate of election and candidature reads: Dr Chothia has shown how the amino sequences of proteins determine their ...
"Intermediate sequences increase the detection of homology between sequences". Journal of Molecular Biology. 273 (1): 349-54. ...
Other potential family members were identified by sequence homology. Chen et al. (2010) reviewed evidence for a new class of ...
Phospholipases A2 can be classified based on sequence homology. Increased levels of lp-PLA2 are associated with cardiac disease ...
De Novo sequencing and homology searching Molecular & Cellular Proteomics. 10.1074/mcp.O111.014902 (2011). Han, X.; He, L.; Xin ... SPIDER is a sequence tag based search tool within PEAKS, which deals with the possible overlaps between the de novo sequencing ... errors and the homology mutations. It reconstructs the real peptide sequence by combining both the de novo sequence tag and the ... PEAKS is commonly used for peptide identification (Protein ID) through de novo peptide sequencing assisted search engine ...
"Intermediate sequences increase the detection of homology between sequences". Journal of Molecular Biology. 273 (1): 349-54. ... Feb 2001). "Initial sequencing and analysis of the human genome" (PDF). Nature. 409 (6822): 860-921. Bibcode:2001Natur.409.. ... "Current status and new features of the Consensus Coding Sequence database". Nucleic Acids Research. 42 (Database issue): D865- ... A structural classification of proteins database for the investigation of sequences and structures" (PDF). Journal of Molecular ...
It was subsequently cloned and sequenced by Radhey Gupta and coworkers. The amino acid sequence showed a strong homology to ... Waldinger D, Eckerskorn C, Lottspeich F, Cleve H (1988). "Amino-acid sequence homology of a polymorphic cellular protein from ... The mitochondrial HSP60 sequence contains a series of G repeats at the C-terminal. The structure and function of this sequence ... The cytoplasmic HSP60 contains a signal sequence of 26 amino acids on the N terminus. This sequence is highly degenerate and is ...
RNA polymerase II regulatory region sequence-specific DNA binding. • DNA binding. • sequence-specific DNA binding. • ... transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific binding. • RNA ... "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences". Proc. Natl. Acad. Sci. U.S.A ... transcription factor activity, sequence-specific DNA binding. • ...
Elastina - Wikipédia, a enciclopédia livre
2009). «Human tropoelastin sequence: dynamics of polypeptide coded by exon 6 in solution». Biopolymers. 91 (11): 943-52. PMID ... Dyksterhuis LB, Weiss AS (2010). «Homology models for domains 21-23 of human tropoelastin shed light on lysine crosslinking». ...
... catalyses strand transfer between a broken sequence and its undamaged homologue to allow re-synthesis of the damaged ... RAD51 is involved in the search for homology and strand pairing stages of the process. ... They each share about 25% amino acid sequence identity with RAD51 and with each other. ...
Integral membrane protein
Homology modeling can be used to construct an atomic-resolution model of the "target" integral protein from its amino acid ... sequence and an experimental three-dimensional structure of a related homologous protein. This procedure has been extensively ...
In 1977, Carl Woese, a microbiologist studying the genetic sequencing of organisms, developed a new sequencing method that ... Engelhardt H; Peters J (1998). "Structural research on surface layers: a focus on stability, surface layer homology domains, ... He sequenced a variety of different species and happened upon a group of methanogens that had vastly different patterns than ... Archaea were first classified as a separate group of prokaryotes in 1977 by Carl Woese and George E. Fox based on the sequences ...
Michael W. Young
A new gene located on chromosome 2 was named timeless (tim) and was successfully cloned and sequenced. They found strong ... "Product of per locus of Drosophila shares homology with proteoglycans". Nature. 320 (6058): 185-188. doi:10.1038/320185a0 ... by determining the sequence of the gene on the X chromosome, they found that the arrhythmic mutation produced a functionless ... protein, while long-period and short-period mutants of per changed the amino acid sequence of a still functional protein.[ ...
They share amino acid sequence homology and core structural similarity to a specific class of major histones but also have ... 3. Complete amino acid sequence of pea seedling histone IV; comparison with the homologous calf thymus histone". The Journal of ... Durrin LK, Mann RK, Kayne PS, Grunstein M (June 1991). "Yeast histone H4 N-terminal sequence is required for promoter ... and compared amino acid sequences of the same histone from different organisms in collaboration with Emil Smith from UCLA. ...
Chand A, Clark J, Cooper CS, Craig IW (1997). "Long-range organization of reiterated sequences, including the SSX1 cDNA at the ... "Fusion of SYT to two genes, SSX1 and SSX2, encoding proteins with homology to the Kruppel-associated box in human synovial ... "The DNA sequence of the human X chromosome". Nature. 434 (7031): 325-37. doi:10.1038/nature03440. PMC 2665286 . PMID 15772651 ... "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences". Proc. Natl. Acad. Sci. U.S.A ...
Index of HIV/AIDS-related articles
... homology (biology) - hormone - host - host factors - HPTN - HPV - HRSA - HTLV-I - HTLV-I-associated myelopathy/tropical spastic ... long terminal repeat sequence (LTR) - long-term nonprogressors - LTR - lumbar - lumbar puncture - lymph - lymph nodes - ...
Specific amino acid sequences (PTS or peroxisomal targeting signal) at the C-terminus (PTS1) or N-terminus (PTS2) of ... Two independent evolutionary analyses of the peroxisomal proteome found homologies between the peroxisomal import machinery and ... The protein receptors, the peroxins PEX5 and PEX7, accompany their cargoes (containing a PTS1 or a PTS2 amino acid sequence, ...
FOXP2 - 维基百科，自由的百科全书
sequence-specific DNA binding transcription factor activity. · sequence-specific enhancer binding RNA polymerase II ... 4.1） Rel homology region（英语：Rel homology domain）. NF-κB（NFKB1、NFKB2、REL、RELA、RELB） · NFAT（C1、C2、C3、C4、5） ... regulation of sequence-specific DNA binding transcription factor activity. · righting reflex. · positive regulation of ...
Brain-derived neurotrophic factor
A common SNP in the BDNF gene is rs6265. This point mutation in the coding sequence, a guanine to adenine switch at ... Fyn associates with the pICD-TrkB through its Src homology domain 2 (SH2) and is phosphorylated at its Y416 site. Once ... January 2009). "Genome-wide association yields new sequence variants at seven loci that associate with measures of obesity". ... evaluation of brain-derived neurotrophic factor genomic DNA sequence variation". American Journal of Medical Genetics. 107 (4 ...
Arqueas, a enciclopedia libre
Molecular Sequences and the Early History of Life. En: Sapp J, editor. "Microbial Phylogeny and Evolution: Concepts and ... Engelhardt H, Peters J (1998). "Structural research on surface layers: a focus on stability, surface layer homology domains, ... "Shotgun sequencing finds nanoorganisms". UCBerkely News (en inglés). Descubrimento do grupo ARMAN de arqueas.. ... Lake JA (xaneiro de 1988). "Origin of the eukaryotic nucleus determined by rate-invariant analysis of rRNA sequences". Nature ...
... ting transfer may be used for homology-based cloning on the basis of amino acid sequence of the protein product of ... Sequences that hybridize with the hybridization probe are further analysed, for example, to obtain the full length sequence of ... A Southern blot is a method used in molecular biology for detection of a specific DNA sequence in DNA samples. Southern ... Particularly useful are the restriction nucleases MspI and HpaII, both of which recognize and cleave within the same sequence. ...
ವಂಶವಾಹಿ - ವಿಕಿಪೀಡಿಯ
International Human Genome Sequencing Consortium (October 2004). "Finishing the euchromatic sequence of the human genome". ... Patterson, C (November 1988). "Homology in classical and molecular biology.". Molecular Biology and Evolution 5 (6): 603-25. ... Min Jou W, Haegeman G, Ysebaert M, Fiers W (May 1972). "Nucleotide sequence of the gene coding for the bacteriophage MS2 coat ... Yu, J. (5 April 2002). "A Draft Sequence of the Rice Genome (Oryza sativa L. ssp. indica)". Science 296 (5565): 79-92. Bibcode: ...
SLAMF6 - ويكيبيديا، الموسوعة الحرة
2006). "The DNA sequence and biological annotation of human chromosome 1". Nature. 441 (7091): 315-21. PMID 16710414. doi: ... "Functional requirements for interactions between CD84 and Src homology 2 domain-containing proteins and their contribution to ... "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences". Proc. Natl. Acad. Sci. U.S.A ...
OPN1LW - Википедија, слободна енциклопедија
2005). „The DNA sequence of the human X chromosome.". Nature. 434 (7031): 325-37. PMC 2665286 . PMID 15772651. doi:10.1038/ ... and coagulation factor VIII genes to an X-Y homology region.". Genomics. 4 (4): 460-71. PMID 2501212. doi:10.1016/0888-7543(89) ... Initial assessment of human gene diversity and expression patterns based upon 83 million nucleotides of cDNA sequence.". Nature ...
Autophagy-related protein 13
1998). "Prediction of the coding sequences of unidentified human genes. X. The complete sequences of 100 new cDNA clones from ... 2008). "Transposition of a reconstructed Harbinger element in human cells and functional homology with two transposon-derived ... 2004). "Complete sequencing and characterization of 21,243 full-length human cDNAs". Nat. Genet. 36 (1): 40-5. doi:10.1038/ ... 2002). "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences". Proc. Natl. Acad. Sci ...
Cyclin-dependent kinase 4
"Identification of CDK4 sequences involved in cyclin D1 and p16 binding". J. Biol. Chem. 272 (30): 18869-74. doi:10.1074/jbc. ... "Homology probing: identification of cDNA clones encoding members of the protein-serine kinase family". Proc. Natl. Acad. Sci. ... "Identification of human and mouse p19, a novel CDK4 and CDK6 inhibitor with homology to p16ink4". Mol. Cell. Biol. 15 (5): ...
Tumor necrosis factor alpha
The sequential and functional homology of TNF and LT led to the renaming of TNF as TNFα (this article) and LT as TNFβ. In 1985 ... positive regulation of sequence-specific DNA binding transcription factor activity. • cellular response to nicotine. • positive ... The binding of TNF to its receptor and its displacement by LT confirmed the functional homology between the two factors. ... expression and homology to lymphotoxin". Nature. 312 (5996): 724-9. Bibcode:1984Natur.312..724P. doi:10.1038/312724a0. PMID ...
Wiskott-Aldrich syndrome protein
In the inactive state, WASp exists in an autoinhibited conformation with sequences near its C-terminus binding to a region near ... It is located towards the C-terminal end of the protein and contains four motifs: two verprolin homology motifs (VV) binds ... Bunnell SC, Henry PA, Kolluri R, Kirchhausen T, Rickles RJ, Berg LJ (October 1996). "Identification of Itk/Tsk Src homology 3 ... A transcript variant arising as a result of alternative promoter usage, and containing a different 5' UTR sequence, has been ...
Brome mosaic virus
The sequence similarities of RNA replication genes and strategies for BMV have been shown to extend to a wide range of plant ... "Sindbis virus proteins nsP1 and nsP2 contain homology to nonstructural proteins from several RNA plant viruses". Journal of ... Ahlquist, P.; Luckow, V.; Kaesberg, P. (1981). "Complete nucleotide sequence of brome mosaic virus RNA3". Journal of Molecular ... French, R.; Ahlquist, P. (1988). "Characterization and engineering of sequences controlling in vivo synthesis of brome mosaic ...
Male reproductive system
This sequence is understandable in light of the fact that both male and female embryos develop within the maternal environment ... 19 July 1990). "A gene from the human sex-determining region encodes a protein with homology to a conserved DNA-binding motif ...
The nucleotide sequence predicts a large prepropeptide with homology to propeptides of other chymotrypsin-like enzymes. J Biol ... Nucleotide sequence and characterization of the gene for secreted alkaline phosphatase from Lysobacter enzymogenes. J Bacteriol ... For example, 16S rDNA phylogenetic analyses show Lysobacter clades that include sequences obtained from hydrothermal vents, ...
The cathelicidin family shares primary sequence homology with the cystatin family of cysteine proteinase inhibitors, ...
Amino acid sequence homology of this isoform of human CASS4 with other family members is 26% overall identity and 42% ... but lacks obvious similarity at the level of primary amino acid sequence. It also lacks a YDYVHL sequence at the N-terminal end ... The CASS4 C-terminus has a short region of CAS family homology, ... Although this lack of sequence similarity may mean a reduced ... proposes several transcriptional regulators for CASS4 based on its promoter region sequence: NF-κβ, p53, LCR-F1 (NFE2-L1, ...
This result calls into question the monophyly of cobras and underscores the uncertainty of the homology of the hood spreading ... based on the amino acid sequences of venom proteins". Molecular Phylogenetics and Evolution. 8 (3): 349-62. CiteSeerX 10.1. ...
The constant domain of the TCR consists of short connecting sequences in which a cysteine residue forms disulfide bonds, which ... "A human T cell-specific cDNA clone encodes a protein having extensive homology to immunoglobulin chains". Nature. 308 (5955): ... Zap70 - a Syk family kinase that binds to ITAM sequences upon tyrosine phosphorylation by Lck and Fyn, and phosphorylates LAT ...
... is the study of stable heritable changes in gene function that do not involve changes in the DNA sequence. The ... "DNA damage, homology-directed repair, and DNA methylation". PLoS Genet. 3 (7): e110. PMC 1913100 . PMID 17616978. doi:10.1371/ ... Leonhardt H, Page AW, Weier HU, Bestor TH (November 1992). "A targeting sequence directs DNA methyltransferase to sites of DNA ... Epigenetic changes modify the activation of certain genes, but not the genetic code sequence of DNA. The microstructure (not ...
Compared to many other sequences, the level of conservation is high, even between B. germanica and D. melanogaster, a highly ... Konopová, Barbora; Zrzavý, Jan (2005-06-01). "Ultrastructure, development, and homology of insect embryonic cuticles". Journal ...
Sequence homology - Wikipedia
Sequence homology is the biological homology between DNA, RNA, or protein sequences, defined in terms of shared ancestry in the ... "quantify the homology." Based on the definition of homology specified above this terminology is incorrect since sequence ... Partial homology can occur where a segment of the compared sequences has a shared origin, while the rest does not. Such partial ... The term "percent homology" is often used to mean "sequence similarity." The percentage of identical residues (percent identity ...
An Introduction to Sequence Similarity ("Homology") Searching
homology, sequence alignment, paralogy, multiple alignment, sequence similarity, sequence evolution, orthlogy Disciplines:. * ... An Introduction to Sequence Similarity ("Homology") Searching Sequence similarity searching, typically with BLAST (units 3.3, ... An Introduction to Sequence Similarity ("Homology") Searching is categorized in the following disciplines: * Science and ... If you know the author of An Introduction to Sequence Similarity ("Homology") Searching, please help us out by filling out the ...
Identifying Cycling Genes by Combining Sequence Homology and Expression Data
free sequence homology search on WWW
... Juergen Brosius RNA.world at uni-muenster.de Sun Mar 31 03:53:13 EST 1996 *Previous ... Please call it sequence SIMILARITY In a search you may find many sequence similarities but only few of the matches may ... 1987) Homology in proteins and nucleic acids: A terminology muddle and a way out of it. Cell 60, 667 *Previous message: free ...
Sequence homology - Wikipedia
Sequence homology is the biological homology between DNA, RNA, or protein sequences, defined in terms of shared ancestry in the ... Alignments of multiple sequences are used to indicate which regions of each sequence are homologous. The term "percent homology ... homology is the conclusion. Sequences are either homologous or not. This involves that the term "percent homology" is a ... "quantify the homology." Based on the definition of homology specified above this terminology is incorrect since sequence ...
Detecting sequence homology at the gene cluster level with MultiGeneBlast. - PubMed - NCBI
Detecting sequence homology at the gene cluster level with MultiGeneBlast.. Medema MH1, Takano E, Breitling R. ... Outline of the homology search process by MultiGeneBlast. First, the amino acid translation of each gene sequence within the ... The tool is fully equipped with applications to generate search databases from GenBank or from the users own sequence data. ... With MultiGeneBlast, we provide a user-friendly and effective tool to perform homology searches with operons or gene clusters ...
Gentle Masking of Low-Complexity Sequences Improves Homology Search
We propose to find homologies by aligning sequences with ... but little research on how to treat them during homology search ... causing strong similarities that are not homologies. There has been much research on identifying low-complexity tracts, ... Detection of sequences that are homologous, i.e. descended from a common ancestor, is a fundamental task in computational ... Sequence similarity searching Is the Subject Area "Sequence similarity searching" applicable to this article? Yes. No. ...
Human : Sequence Homology, Antibody Reactivity | Cell Signaling
'sequence homology' Protocols and Video...
... sequence homology include Genetic Manipulation in Δku80 Strains for Functional Genomic Analysis of Toxoplasma gondii, ... Using RNA-sequencing to Detect Novel Splice Variants Related to Drug Resistance in In Vitro Cancer Models, Identification of ... Identification of Rare Bacterial Pathogens by 16S rRNA Gene Sequencing and MALDI-TOF MS, Targeted in Situ Mutagenesis of ... Sequencing Metagenomes and Metatranscriptomes from Complex Animal-associated Samples, Quantitation and Analysis of the ...
Protein backbone angle restraints from searching a database for chemical shift and sequence homology. - PubMed - NCBI
Protein backbone angle restraints from searching a database for chemical shift and sequence homology.. Cornilescu G1, Delaglio ... TALOS yields the 10 triplets which have the closest similarity in secondary chemical shift and amino acid sequence to those of ... the query sequence. If the central residues in these 10 triplets exhibit similar phi and psi backbone angles, their averages ... of the weighting factors attached to the secondary chemical shifts of the five types of resonances relative to that of sequence ...
MIPS: a database for protein sequences, homology data and yeast genome information
... distributes protein sequence data within the framework of the tripartite association of the PIR-International Protein Sequence ... Martinsried Institute for Protein Sequences) at the Max-Planck-Institute for Biochemistry, Martinsried near Munich, Germany, ... MIPS: a database for protein sequences, homology data and yeast genome information Nucleic Acids Res. 1997 Jan 1;25(1):28-30. ... homology data and to yeast genome information. (i) Sequence similarity results from the FASTA program () are stored in the ...
Amino Acid Sequence Homology - Medical Dictionary online-medical-dictionary.org
Gene conservation in Bacillus species. I. Conserved genetic and nucleic acid base sequence homologies | PNAS
Sequence homology between certain viral proteins and proteins related to encephalomyelitis and neuritis | Science
Sequence homology between certain viral proteins and proteins related to encephalomyelitis and neuritis ... Sequence homology between certain viral proteins and proteins related to encephalomyelitis and neuritis ... Sequence homology between certain viral proteins and proteins related to encephalomyelitis and neuritis ... Sequence homology between certain viral proteins and proteins related to encephalomyelitis and neuritis ...
Homology-Driven Proteomics of Dinoflagellates with Unsequenced Genomes Using MALDI-TOF/TOF and Automated De Novo Sequencing
... Da ... J. A. Taylor and R. S. Johnson, "Sequence database searches via de Novo peptide sequencing by tandem mass spectrometry," Rapid ... "Sequence similarity-driven proteomics in organisms with unknown genomes by LC-MS/MS and automated de novo sequencing," ... "Sequence similarity-driven proteomics in organisms with unknown genomes by LC-MS/MS and automated de novo sequencing," ...
Experts and Doctors on amino acid sequence homology in China
Publications about Experts and Doctors on amino acid sequence homology in China ... Experts and Doctors on amino acid sequence homology in China. Summary. Locale: China ... Experts and Doctors on molecular sequence data in China*Experts and Doctors on amino acid sequence in China*Experts and Doctors ... You are here: Locale , Experts and Doctors on amino acid sequence homology in China ...
Structure-activity analysis of thanatin, a 21-residue inducible insect defense peptide with sequence homology to frog skin...
Immune challenge to the insect Podisus maculiventris induces synthesis of a 21-residue peptide with sequence homology to frog ... Structure-activity analysis of thanatin, a 21-residue inducible insect defense peptide with sequence homology to frog skin ... Structure-activity analysis of thanatin, a 21-residue inducible insect defense peptide with sequence homology to frog skin ... Structure-activity analysis of thanatin, a 21-residue inducible insect defense peptide with sequence homology to frog skin ...
Relationship Between Sequence Homology, Genome Architecture, and Meiotic Behavior of the Sex Chromosomes in North American...
In contrast, homology is concentrated in high complexity, and presumably euchromatic, sequence on the X and Y chromosomes of ... Relationship Between Sequence Homology, Genome Architecture, and Meiotic Behavior of the Sex Chromosomes in North American ... Relationship Between Sequence Homology, Genome Architecture, and Meiotic Behavior of the Sex Chromosomes in North American ... Relationship Between Sequence Homology, Genome Architecture, and Meiotic Behavior of the Sex Chromosomes in North American ...
at.algebraic topology - homology of a base space of a a fiber sequence - MathOverflow
... and suppose we know the homology of A and B, is there a homological spectral sequence converging to the homology of $C$. ... begingroup$ Often the information on the homology of $C$ can be understood from the Serre spectral sequence. But this is nit ... homology of a base space of a a fiber sequence. Ask Question ... Serre spectral sequence degeneration in homology vs cohomology ... There are spectral sequences of this sort for certain fiber sequences. For example, if $A$ is a topological group and $B \ ...
Sequence Similarity - 1BMX: HIV-1 CAPSID PROTEIN MAJOR HOMOLOGY REGION PEPTIDE ANALOG, NMR, 8 STRUCTURES Sequence...
... capsid protein major-homology-region peptide analogs by NMR spectroscopy. ... Structures of protein chains with identical sequences (sequence identity > 95%) are aligned, superimposed and clustered. ... Sequence Similarity Clusters for the Entities in PDB 1BMX Legend Entity #1 , Chains: A HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 ... Blast this sequence against all of PDB Archive.. Rank. In each cluster, the chains are sorted (i.e. ranked) according to the ...
Homology sequence analysis using GPU acceleration
I have developed a method to accelerate sequence alignment on the GPU, and I used the method to investigate whether the ... of various parallel computing platforms to several problems in the detection and analysis of homology in biological sequence. I ... it is possible to deduce information from raw sequences without supplying the underlying prior knowledge to come up with an ... a framework to scaffold shared sequence motifs across large numbers of genomes to illuminate the structure of the regulatory ...
Sequence homology and microhomology dominate chromosomal double-strand break repair in African trypanosomes
Variability in Coat Protein Sequence Homology Among American and European Sources of Strawberry Vein Banding Virus
GHOSTX: An Improved Sequence Homology Search Algorithm Using a Query Suffix Array and a Database Suffix Array
We designed a new homology search algorithm that finds seed sequences based on the suffix arrays of a query and a database, and ... However, huge amounts of sequence data create the problem that even general homology search analyses using BLASTX become ... This explosion of sequence data makes computational analysis with contemporary tools more difficult. We offer this tool as a ... sequencing technology continues to improve, and sequencers are increasingly producing larger and larger quantities of data. ...
Model for the phycobilisome rod with interlocking disks based on domain-weighted linker-polypeptide sequence homologies of...
Sequence homology in eukaryotes (SHOE): interactive visual tool for promoter analysis | BMC Genomics | Full Text
Microarray and DNA-sequencing based technologies continue to produce enormous amounts of data on gene expression. This data has ... Sequence homology in eukaryotes (SHOE): interactive visual tool for promoter analysis. *Natalia Polouliakh1, 2, 3Email author ... Open source public matrices are matched to the human sequence if mouse and rat are aligned to human sequence region with ... Gotoh O. An improved algorithm for matching biological sequences. J Mol Biol. 1982;162(3):705-8.View ArticleGoogle Scholar. ...
Amino acid sequence homology between Piv, an essential protein in site-specific DNA inversion in Moraxella lacunata, and...
Amino acid sequence homology between Piv, an essential protein in site-specific DNA inversion in Moraxella lacunata, and ... Amino acid sequence homology between Piv, an essential protein in site-specific DNA inversion in Moraxella lacunata, and ... Amino acid sequence homology between Piv, an essential protein in site-specific DNA inversion in Moraxella lacunata, and ... Amino acid sequence homology between Piv, an essential protein in site-specific DNA inversion in Moraxella lacunata, and ...
Nucleotide sequences of the genes regulating O-polysaccharide antigen chain length (rol) from Escherichia coli and Salmonella...
The homology between the nucleotide sequences of these two genes was found to be 68.9%. Both the E. coli rol and S. typhimurium ... The homology between these deduced polypeptide sequences was observed to be 72%. A complementation test was performed in which ... Nucleotide sequences of the genes regulating O-polysaccharide antigen chain length (rol) from Escherichia coli and Salmonella ... Nucleotide sequences of the genes regulating O-polysaccharide antigen chain length (rol) from Escherichia coli and Salmonella ...
Abstract: Opriessnig T. 2005;13(5):246-253 Genomic homology of ORF 5 gene sequence between modified
Genomic homology of ORF 5 gene sequence between modified live vaccine virus and porcine reproductive and respiratory syndrome ... Genomic homology of ORF 5 gene sequence between modified live vaccine virus and porcine reproductive and respiratory syndrome ... sequencing of open reading frame (ORF) 5, these three isolates vary considerably from each other (72% to 86% homology) and from ... Implication: Under the conditions of this study, the degree of ORF 5 homology between the MLV PRRSV vaccine and the infecting ...
Homology-Dependent Maternal Inhibition of Developmental Excision of Internal Eliminated Sequences inParamecium tetraurelia |...
Its sequence was shown to be identical with the A29 germ line sequence, which differs from the A51 germ line sequence by one ... Homology-Dependent Maternal Inhibition of Developmental Excision of Internal Eliminated Sequences inParamecium tetraurelia. ... The homology requirement can nevertheless tolerate small differences between the sequence present in the maternal macronucleus ... Sequences of the ends of tested IESs. The left (L) and right (R) end sequences of each IES are aligned with the degenerate ...
AlignmentsAlignmentHomologous SequencesCDNAGeneGenesBioinformaticsGenomesPercent homologyPeptidesComplete nucleotide sequenceProteins and nucleic acidsAmino acidsDegree of similarity between sequencesPutativeProtein sequenceHigh-homologyDefinition of homologyRemote homologyOverall homologyNucleotide sequencesPhylogeneticNovoNucleicSignificant similarityHomologsPeptideGenome sequencesDetectionNucleotidesSpeciesResiduesStructuralSpecificityBased on sequence similarityClustersDetectHumansPredictionConvergent evolutionBiologyMammalsAnalysesPartialDataAntigenBLASTSimilaritiesRecombinationConservationSimilar sequences
- Alignments of multiple sequences are used to indicate which regions of each sequence are homologous. (wikipedia.org)
- Sequence similarity searches, multiple sequence and structural alignments generation and editing, and even the possibility to merge sequence and structure alignments have been implemented in PyMod, with the aim of creating a simple, yet powerful tool for sequence and structure analysis and building of homology models. (biomedcentral.com)
- OPTIMAL SEQUENCE ALIGNMENTS Given any two sequences, there are an enormous number of ways they can be aligned if one allows for insertions and deletions (collectively referred to as indels or gaps) in the alignment. (sciencedocbox.com)
- Users can perform taxonomic, functional or comparative analysis, map reads to reference sequences, reference-based multiple alignments and reference-guided assembly and integrate their own classifications. (omictools.com)
- Researchers at Brigham Young University have developed biologically informative features that can be extracted from multiple sequence alignments of putative homologous genes (orthologs and paralogs) and further utilized in context of guided experimentation to verify false positive outcomes. (rna-seqblog.com)
- They demonstrate that their machine learning method trained on both known homology clusters obtained from OrthoDB and randomly generated sequence alignments (non-homologs), successfully determines apparent false positives inferred by heuristic algorithms especially among proteomes recovered from low-coverage RNA-seq data. (rna-seqblog.com)
- Pfam is a comprehensive collection of protein domains and families, represented as multiple sequence alignments and as profile hidden Markov models. (psu.edu)
- These new options of MAFFT showed higher accuracy than currently available methods including TCoffee version 2 and CLUSTAL W in benchmark tests consisting of alignments of.50 sequences. (psu.edu)
- A sequence alignment of mammalian histone proteins. (wikipedia.org)
- Is the Subject Area "Sequence alignment" applicable to this article? (plos.org)
- I have developed a method to accelerate sequence alignment on the GPU, and I used the method to investigate whether the Operational Taxonomic Unit (OTU) classification problem can be improved with such sheer amount of computational power. (umsystem.edu)
- Accurate multiple sequence‐structure alignment of RNA sequences using combinatorial optimization. (currentprotocols.com)
- A sequence alignment, based on the idea that residues equivalent in the primordial catalytic GH-H/GH31 (β/α)8-barrel may not be found in the present-day GH-H and GH31 structures at strictly equivalent positions, shows remote sequence homologies covering β3, β4, β7 and β8 of the GH-H and GH31 (β/α)8-barrels. (dtu.dk)
- The ease of use, integration with many sequence retrieving and alignment tools and PyMOL, one of the most used molecular visualization system, are the key features of this tool. (biomedcentral.com)
- Each tool must be considered as standalone (e.g., it's possible to perform a sequence alignment task without searching in the database as a mandatory step). (biomedcentral.com)
- PyMod has a rich functionality, based on its core sequence alignment, clustering and editing window. (biomedcentral.com)
- 27: C 2009 by John Wiley & Sons, Inc. Keywords: sequence similarity homology dynamic programming similarity-scoring matrices sequence alignment multiple alignment sequence evolution AN INTRODUCTION TO IDENTIFYING HOMOLOGOUS SEQUENCES Upon determining a new sequence, one common objective is to assign a function to that sequence, or perhaps multiple functions to various subsequences. (sciencedocbox.com)
- Fortunately, there is a simple method, known as dynamic programming (DP), to determine the score of the best possible alignment between two sequences. (sciencedocbox.com)
- 2 Seq B: b 1 Seq A: a 1 a 2 b 2 ai an b j b m S(i 1, j 1) S(i, j 1) S(i 1, j) S(i, j) S(i,j) max S(i 1, j 1) score(a i, b j ) S(i, j 1) S(i 1, j) Figure Dynamic programming algorithm for optimum sequence alignment. (sciencedocbox.com)
- Once the top row and first column are initialized, the entire matrix can be filled following the simple rule shown in Figure 3.1.1, and the score of the best possible alignment of the two sequences is the element in the lower right corner of the matrix, S(n,m). (sciencedocbox.com)
- Based on the strategy used for comparing reads with sequences/pre-computed models, taxonomy-dependent methods can be sub-classified into alignment-based, composition-based and hybrid methods. (omictools.com)
- CLUSTALW program was used for sequence alignment and phylogenic tree creation. (scitechnol.com)
- Uncertainty in homology inferences: assessing and improving genomic sequence alignment. (ox.ac.uk)
- Sequence alignment underpins all of comparative genomics, yet it remains an incompletely solved problem. (ox.ac.uk)
- To our knowledge, this is the first nonheuristic algorithm for DNA sequence alignment to show robust improvements over the classic Needleman-Wunsch algorithm. (ox.ac.uk)
- Methods: The genome of M. leprae was annotated using sequence alignment tools to identify DNA repair genes that have homologs in Mycobacterium tuberculosis and Escherichia coli. (iith.ac.in)
- 2005 MAFFT version 5: improvement in accuracy of multiple sequence alignment. (psu.edu)
- The accuracy of multiple sequence alignment pro-gram MAFFT has been improved. (psu.edu)
- For a multiple alignment consisting of 8 sequences with low similarity, the accuracy was improved (2-10 percentage points) when the sequences were aligned together with dozens of their close homologues (E-value, 105-1020) col-lected from a database. (psu.edu)
- The Clustal series of programs are widely used in molecular biology for the multiple alignment of both nucleic acid and protein sequences and for preparing phylogenetic trees. (psu.edu)
- The third generation of the series, ClustalW =-=(10)-=-, released in 1994, incorporated a number of improvements to the alignment algorithm, including sequence weighting, position-specific gap penalties and the automatic choice of a suitable residue compa. (psu.edu)
- See sequence clustering and sequence alignment . (wikidoc.org)
- At that homology level, there are likely to be only a few gaps in the alignment, the alignment is likely to be accurate, and the template's 3D structure is likely to be close to the actual target structure. (bio.net)
- DESCRIPTION: MODELLER is most frequently used for homology or comparative modeling of protein three-dimensional structure: the user provides an alignment of a sequence to be modeled with known related structures and MODELLER will automatically calculate a full-atom model. (bio.net)
- Sequence-structure alignment can be used as an alternative search strategy. (biomedcentral.com)
- In this scenario, the query consists of a base pairing probability matrix, which can be derived either from a single sequence or from a multiple alignment representing a set of known representatives. (biomedcentral.com)
- As a search engine we devised a semi-global scanning variant of LocARNA 's algorithm for sequence-structure alignment. (biomedcentral.com)
- 1. Pairwise Global Alignment of Sequences. (wiley.com)
- 1.9 Alignment Score and Sequence Distance. (wiley.com)
- Homologous sequences are orthologous if they are inferred to be descended from the same ancestral sequence separated by a speciation event: when a species diverges into two separate species, the copies of a single gene in the two resulting species are said to be orthologous. (wikipedia.org)
- 1 An Introduction to Sequence Similarity ( Homology ) Searching Gary D. Stormo 1 UNIT Washington University, School of Medicine, St. Louis, Missouri ABSTRACT Homologous sequences usually have the same, or very similar, functions, so new sequences can be reliably assigned functions if homologous sequences with known functions can be identified. (sciencedocbox.com)
- Because homologous sequences, those related by common ancestry, generally have the same or very similar functions, their identification can be used to infer the function of the new sequence. (sciencedocbox.com)
- The methods for identifying homologous sequences rely on finding similarities between sequences that are unlikely to happen by chance, thereby allowing the inference that the sequences have evolved from a common ancestor. (sciencedocbox.com)
- Due to only using heuristic filtering based on significance score cutoffs and having no cluster post-processing tools available, these methods can often produce multiple clusters constituting unrelated (non-homologous) sequences. (rna-seqblog.com)
- Many algorithms exist to cluster protein sequences into sequence families, which are sets of mutually homologous sequences. (wikidoc.org)
- Homologous sequences are of two types: orthologous and paralogous. (wikidoc.org)
- Double-stranded cDNA of potato virus X (PVX) genomic RNA has been cloned and sequenced. (uniprot.org)
- The complete sequence of 354 amino acids for the mature enzyme was determined by sequencing both cDNA and protein. (lu.se)
- In the present study, an activated m phi cDNA library yielded new Nramp clones that differ in the 5' region from the published pre-B cell-derived clone sequence, resulting in addition of 64 amino acids at the NH2 terminus of the predicted protein. (rupress.org)
- The nucleotide sequence of a cloned cDNA insert carried by pHDQ14 was determined and found to code for the 107 C-terminal amino acids of rat liver cytochrome P-450e. (unibas.ch)
- Comparison of the pHQ14 cDNA sequence with those of cloned cDNAs for cytochrome P-450b and of 2 P-450e-like genes revealed segmental homologies that may have resulted from gene conversion. (unibas.ch)
- We therefore sequenced and characterized the RFG8 cDNA, which showed no significant similarity to any functional protein described as yet. (aacrjournals.org)
- We have cloned and sequenced the gene and the full-length cDNA coding for the major endoglucanase EG-I, and compared this to the cbhl gene sequence to clarify the relationship between the EG and CBH classes of cellulases. (vtt.fi)
- Cloning, expression, and sequence homologies of cDNA for human carbonic anhydrase II. (elsevier.com)
- Contig sequences are obtained by assemblying 5' EST sequence, 3' EST sequence, 5' EST-3'EST-ligated sequence and full-length cDNA sequence by the assembly program Phrap ( http://www.phrap.org/index.html ). (biosciencedbc.jp)
- Sequence of a rat immunoglobulin gamma 2c heavy chain constant region cDNA: extensive homology to mouse gamma 3. (ox.ac.uk)
- The complete sequence of the rat immunoglobulin gamma 2c heavy chain constant region has been determined by cDNA cloning and by mRNA sequencing. (ox.ac.uk)
- Such partial homology may result from a gene fusion event. (wikipedia.org)
- Detecting sequence homology at the gene cluster level with MultiGeneBlast. (nih.gov)
- With MultiGeneBlast, we provide a user-friendly and effective tool to perform homology searches with operons or gene clusters as basic units, instead of single genes. (nih.gov)
- First, the amino acid translation of each gene sequence within the query gene cluster is searched against the selected MultiGeneBlast database, yielding a data set of BLAST hits. (nih.gov)
- The first example output shown here displays a homology search for the coumermycin biosynthetic gene cluster, which identifies gene clusters encoding related compounds. (nih.gov)
- citation needed] Given their tremendous importance for biology and bioinformatics, orthologous genes have been organized in several specialized databases that provide tools to identify and analyze orthologous gene sequences. (wikipedia.org)
- Strawberry vein banding virus (SVBV) isolates from North America, Czech Republic, Norway, and Germany were collected and their variability was determined by dot blot hybridization and confirmed by sequencing of a 431-nucleotide fragment from the middle part of the coat protein gene. (apsnet.org)
- Microarray and DNA-sequencing based technologies continue to produce enormous amounts of data on gene expression. (biomedcentral.com)
- The E. coli and S. typhimurium rol gene sequences consist of 978 and 984 nucleotides, respectively. (asm.org)
- sequence specificity is complete both between genes and between different IESs in the same gene. (asm.org)
- Nucleotide sequence of the leukotoxin gene from Actinobacillus actinomycetemcomitans: homology to the alpha-hemolysin/leukotoxin gene family. (asm.org)
- We now present the complete nucleotide sequence of the lktA gene from A. actinomycetemcomitans. (asm.org)
- Analysis of the kinetics of hybridization of these probes in homologous and heterologous complementary DNA-RNA hybridization reactions has shown that the sequence of the smallest RNA (RNA 4), which contains the coat protein gene, is present within RNA 3. (eurekamag.com)
- The sequence of the pckA gene coding for phosphoenolpyruvate carboxykinase in E. coli K-12 and previous MW determinations indicate that this allosteric enzyme is a monomer of MW 51 316. (eurekamag.com)
- I have the amino acid sequence of a gene of interest. (biostars.org)
- Studies of AMINO ACID SEQUENCE HOMOLOGY and NUCLEIC ACID SEQUENCE HOMOLOGY provide useful information about the genetic relatedness of genes, gene products, and species. (childrensmercy.org)
- It is likely that the sequence exchange is mediated by gene conversion, rather than actual physical translocation. (barnardhealth.us)
- Accurate detection of homologous relationships of biological sequences (DNA or amino acid) amongst organisms is an important and often difficult task that is essential to various evolutionary studies, ranging from building phylogenies to predicting functional gene annotations. (rna-seqblog.com)
- These results suggest that gene conversion may generate sequence variants of genes for rat liver cytochrome P-450s. (unibas.ch)
- However, gene sequencing is only the beginning. (biomedcentral.com)
- Although determination of the sequence of every gene in Volvox or any other species allows a better understanding of the organism's physiological potential, it is just the first step of a complete description of how the organism works. (biomedcentral.com)
- The sequence was a 93,629-bp plasmid encoding a single antimicrobial drug resistance gene, bla CTX-M-14 . (cdc.gov)
- While the analysis presented in [ 9 ] for Vibrionaceae was the most comprehensive to date (eight gene loci for 95 Vibrionaceae species) and provided the a hypothesis for a phylogenetic taxonomy for the group, the number of genomes already sequenced for Vibrionaceae lends itself to a genome-level analysis. (biomedcentral.com)
- Significant sequence similarity and shared functional domains indicate that these two genes are orthologous genes,  inherited from the shared ancestor . (wikipedia.org)
- Sequence similarity searches can identify "homologous" proteins or genes by detecting excess similarity - statistically significant similarity that reflects common ancestry. (merlot.org)
- Edges between genes represent sequence similarity. (cmu.edu)
- As we show, by incorporating sequence similarity information we were able to obtain a more accurate set of genes compared to methods that rely on expression data alone. (cmu.edu)
- Nucleotide sequences of the genes regulating O-polysaccharide antigen chain length (rol) from Escherichia coli and Salmonella typhimurium: protein homology and functional complementation. (asm.org)
- In this article, we report on the nucleotide sequences of the rol genes of Escherichia coli O75 and Salmonella typhimurium LT2. (asm.org)
- The term homology is also used in a non-evolutionary sense in terms of homologous chromosomes , meaning a pair of non-identical chromosomes from a diploid organism that can pair (synapse) during meiosis , or regions of chromosomes with the same set of genes. (newworldencyclopedia.org)
- Motivation: When predicting sequence features like transmembrane topology, signal peptides, coil--coil structures, protein secondary structure or genes, extra support can be gained from homologs. (psu.edu)
- The current study is aimed at understanding the sequence and functional annotation of DNA repair genes in M. leprae. (iith.ac.in)
- Analysis of the genome sequence of Arabidopsis indicates the presence of 34 CDPK genes ( The Arabidopsis Genome Initiative, 2000 ). (plantphysiol.org)
- In genetics , homology can be observed in DNA sequences that code for proteins (genes) and in noncoding DNA. (wikidoc.org)
- For protein coding genes, one can compare translated amino-acid sequences of different genes. (wikidoc.org)
- Genes that share a high sequence identity or similarity support the hypothesis that they share a common ancestor and are therefore homologous. (wikidoc.org)
- For example, in general, if two or more genes have highly similar DNA sequences, it is likely that they are homologous. (wikidoc.org)
- 1. A marker DR-beta-I DNA sequence from the HLA class II beta genes associated with insulin-dependent diabetes mellitus and with DR4-associated susceptibility to Pemphigus vulgaris. (google.com.au)
- 5. Marker DQ-beta DNA sequences from the HLA class II beta genes associated with DRw6-associated susceptibility to Pemphigus vulgaris. (google.com.au)
- Comparison with other heavy chain genes reveals a high degree of homology (87%) to mouse gamma 3 and suggests that rat and mouse gamma genes separated from a common set of three ancestral genes. (ox.ac.uk)
- Once confined only to experts in bioinformatics, protein sequence retrieving, aligning and modeling tasks are now being routinely approached by an increasing number of researchers, who can take also advantage of the growing number of structures that are being deposited every day in public databases. (biomedcentral.com)
- Homology among proteins and DNA is often concluded on the basis of sequence similarity, especially in bioinformatics . (wikidoc.org)
- I have developed a method to accelerate pairwise k-mer comparison on the GPU, and I used the method to further develop PolyHomology, a framework to scaffold shared sequence motifs across large numbers of genomes to illuminate the structure of the regulatory network in yeasts. (umsystem.edu)
- The patchy homologies are similar to those found earlier during the analyses of some of the junction sequences in integrated Ad12 genomes in Ad12-induced hamster tumor cell lines. (uni-muenchen.de)
- Three of the genomes included in the 44 taxon dataset, those of Vibrio gazogenes , Salinivibrio costicola , and Aliivibrio logei have been newly sequenced and their genome sequences are documented here. (biomedcentral.com)
- De novo sequencing of peptides using MALDI/TOF-TOF," Journal of the American Society for Mass Spectrometry , vol. 13, no. 7, pp. 784-791, 2002. (hindawi.com)
- Immune challenge to the insect Podisus maculiventris induces synthesis of a 21-residue peptide with sequence homology to frog skin antimicrobial peptides of the brevinin family. (pnas.org)
- The extent of immunological similarity between tetanus toxin and botulinum toxins A, B, C1, and E was studied by using 10 antibodies produced against synthetic peptides representing different sequences of tetanus toxin, mouse antitetanus serum, and human Tetanus Immune Globulin. (asm.org)
- The use of recombinant peptides based upon the repeated amino acid sequences of Plasmodium has been proposed for malaria vaccines. (ajtmh.org)
- Such antibodies and peptides encoded by said DNA sequences can be used therapeutically or prophylactically. (google.com.au)
- These peptides all show significant amino acid sequence homology to atracotoxin-Hvf17 (ACTX-Hvf17), a non-toxic peptide isolated from the venom of H. versuta, and a variety of AVIT family proteins including mamba intestinal toxin 1 (MIT1) and its mammalian and piscine orthologs prokineticin 1 (PK1) and prokineticin 2 (PK2). (edu.au)
Complete nucleotide sequence3
- The complete nucleotide sequence of potato virus X and its homologies at the amino acid level with various plus-stranded RNA viruses. (uniprot.org)
- Peanut bud necrosis tospovirus S RNA: complete nucleotide sequence, genome organization and homology to other tospoviruses. (icrisat.org)
- The complete nucleotide sequence of the S RNA of peanut bud necrosis virus (PBNV) has been determined. (icrisat.org)
Proteins and nucleic acids1
- 1987) Homology in proteins and nucleic acids: A terminology muddle and a way out of it. (bio.net)
- The degree of similarity between sequences of Amino Acids . (online-medical-dictionary.org)
- Matches of at least 4 amino acids were found for all sequences. (ajtmh.org)
- This new domain is rich in proline, serine, and basic amino acids, and includes three protein kinase C phosphorylation sites and a putative Src homology 3 binding domain. (rupress.org)
- The deduced 437-amino acids (aa) long EG-I protein with a 22-aa long signal peptide is 45% identical in aa sequence with CBH-I. The best conserved region is found at the C terminus and shows about 70% homology. (vtt.fi)
- The WH2 (WASP-Homology 2, or Wiskott-Aldrich homology 2) domain is an ~18 amino acids actin-binding motif. (wikipedia.org)
Degree of similarity between sequences1
- The degree of similarity between sequences. (jove.com)
- The significance of these homologies with respect to putative functions of the PVX-encoded proteins are discussed. (uniprot.org)
- Human prostatic and lysosomal acid phosphatases exhibit 50% sequence homology, including five Cys residues and two putative N-linked glycosylation sites. (lu.se)
- NH2-terminal sequence of macrophage-expressed natural resistance-associated macrophage protein (Nramp) encodes a proline/serine-rich putative Src homology 3-binding domain. (rupress.org)
- Almost ~42 % and ~25 % of predicted putative homologies by InParanoid and HaMStR respectively were classified as false positives on experimental data set. (rna-seqblog.com)
- The deduced EG-I sequence contains six putative N-glycosylation sites, and a putative O-glycosylated region is found near the C terminus, closely resembling a similar region at the C terminus of CBH-I. Comparison of the aa sequences suggests that the evolutionary divergence of EG-I from CBH-I has involved four separate 10-20 aa "deletions" from the ancestral protein. (vtt.fi)
- Sequence-based computational methods offer a viable, cost-effective way to identify putative RNA-binding residues in RNA-binding proteins. (paperity.org)
- MIPS contributes nearly 50% of the data input to the PIR-International Protein Sequence Database. (nih.gov)
- N. S. Tannu and S. E. Hemby, " De novo protein sequence analysis of Macaca mulatta ," BMC Genomics , vol. 8, no. 1, article 270, 2007. (hindawi.com)
- Can a protein sequence be assigned to multiple orthologous groups in eggNOG? (biostars.org)
- I am wondering why the same protein sequence can appear in multiple orthologous groups _within th. (biostars.org)
- It first uses PSIPRED to predict the secondary structure for each protein sequence. (ntu.edu.sg)
- In recent years, an exponential growing number of tools for protein sequence analysis, editing and modeling tasks have been put at the disposal of the scientific community. (biomedcentral.com)
- Integrating protein sequence and structure information has therefore become an imperative, especially in the field of protein structure prediction from sequence, by means of homology modeling (HM) methodologies. (biomedcentral.com)
- In recent years, a number of valuable tools related to protein sequence analysis and modeling (e.g. (biomedcentral.com)
- Contrary to current motif detection procedures we use a feature based protein sequence representation we developed earlier. (uni-bielefeld.de)
- Specifically, marker DNA sequences which detect either directly or indirectly the identity of the codon encoding for the amino acid at position 57 of the DQ-beta protein sequence are disclosed as well as sequences from the DR-beta region. (google.com.au)
- 7. A marker DNA sequence from the HLA DQ-beta allele associated with susceptibility to insulin-dependent diabetes mellitus, wherein said sequence can be used to detect either directly or indirectly the identity of the codon at position 57 of the DQ-beta protein sequence. (google.com.au)
- Provides a comprehensive introduction to the analysis of protein sequence and structure analysis. (wiley.com)
- We identified multiple specific regions in SARS-CoV-2 that have high homology to the SARS-CoV virus. (cdc.gov)
Definition of homology3
- Based on the definition of homology specified above this terminology is incorrect since sequence similarity is the observation, homology is the conclusion. (wikipedia.org)
- Such a definition of homology is a redefinition from the classical understanding of the term, which predated Charles Darwin 's theory of evolution , having been coined by Richard Owen in the 1840s. (newworldencyclopedia.org)
- Furthermore, he finds even retaining the pre-Darwinian definition of homology as structural similarity problematic because of such factors as the lack of correspondence between homology and development pathways, since there are examples of similar structures in adult forms where ancestry is assumed that actually are products of radically different development processes. (newworldencyclopedia.org)
- Discriminative remote homology detection. (metu.edu.tr)
- We define a new pairwise sequence comparison scheme, for distantly related proteins and report its performance on remote homology detection task. (metu.edu.tr)
- Currently probabilistic models of protein families, namely HMMs, are the methodology of choice for remote homology analysis. (uni-bielefeld.de)
- Such small building blocks are automatically combined to global protein family HMMs which can be applied to remote homology analysis tasks. (uni-bielefeld.de)
- The results of an experimental evaluation on a challenging task of remote homology classification prove that robust models containing substantially smaller amounts of parameters can be estimated using the new modeling approach. (uni-bielefeld.de)
- Despite the overall homology to the other leukotoxin/hemolysin proteins, the LktA protein from A. actinomycetemcomitans has several unique properties. (asm.org)
- This precondition provides restrictions to the search for candidate exons concerning their length, splice site conservation and reading frame preservation, and overall homology. (biomedcentral.com)
- 6. The marker DQ-beta DNA sequences of claim 5 which comprise one or more nucleotide sequences from the second exon of the DQB1.3 allele from about codon 20 to about codon 80. (google.com.au)
- Orthologous sequences provide useful information in taxonomic classification and phylogenetic studies of organisms. (wikipedia.org)
- These resources employ approaches that can be generally classified into those that use heuristic analysis of all pairwise sequence comparisons, and those that use phylogenetic methods. (wikipedia.org)
- They have all been sequenced de novo using RNA-seq and there's no genome sequences available from the species I'm working with. (biostars.org)
- Therefore sequencing data extracted from incomplete genome/transcriptome assemblies originated from low coverage sequencing or produced by de novo processes without a reference genome are susceptible to high false positive rates of homology detection. (rna-seqblog.com)
- Significant similarity is strong evidence that two sequences are related by evolutionary changes from a common ancestral sequence. (wikipedia.org)
- This unit provides an overview of the inference of homology from significant similarity, and introduces other units in this chapter that provide more details on effective strategies for identifying homologs. (merlot.org)
- Homology is inferred based on sequence similarity, and many methods have been developed to identify sequences that have statistically significant similarity. (sciencedocbox.com)
- The units in this Chapter all address aspects of this problem, finding significant similarity between new sequences and those that are currently in the databases of known sequences. (sciencedocbox.com)
- A particular difficulty is posed by divergent homologs that have lost recognizable sequence similarity. (biomedcentral.com)
- Although highly reliable, HomPRIP cannot make predictions for the unaligned parts of query proteins and its coverage is limited by the availability of close sequence homologs of the query protein with experimentally determined RNA-binding sites. (paperity.org)
- By reducing homologies of such peptide vaccines to host proteins, the possibility of autoimmune complications may be reduced, and the effective immune response may be enhanced. (ajtmh.org)
- 19 taxa) and one for which the genome sequences contain multiple contigs (44 taxa). (biomedcentral.com)
- The premise of this research is to investigate the applicability of various parallel computing platforms to several problems in the detection and analysis of homology in biological sequence. (umsystem.edu)
- Here we ask two related questions: (1) Is secondary structure alone informative for homology search and the detection of novel members of RNA classes? (biomedcentral.com)
- The sequence [6435 nucleotides excluding the poly(A) tract] revealed five open reading frames (ORFs) which were numbered one to five starting at the 5' terminus of the RNA. (uniprot.org)
- One ORF (1 320 nucleotides in the viral sense strand) encodes a Mr 49.5 kDa protein, identified as the nonstructural (NSs) protein based on similarity to published tospovirus sequences. (icrisat.org)
- To this end, we developed a novel, reference-blind computational method to analyze sparse sequencing data from flow-sorted X and Y chromosomes isolated from vole species with sex chromosomes that always ( Microtus montanus ), never ( Microtus mogollonensis ), and occasionally synapse ( Microtus ochrogaster ) at meiosis. (genetics.org)
- Unexpectedly, we find more shared X/Y homology in the two vole species with no and sporadic X/Y synapsis compared to the species with obligate synapsis. (genetics.org)
- Sex chromosome homology in the asynaptic and occasionally synaptic species is interspersed along chromosomes and largely restricted to low-complexity sequences, including a striking enrichment for the telomeric repeat sequence, TTAGGG. (genetics.org)
- In contrast, homology is concentrated in high complexity, and presumably euchromatic, sequence on the X and Y chromosomes of the synaptic vole species, M. montanus . (genetics.org)
- Cloning of the complete coding region of PRG1 revealed that it shared a high degree of amino acid sequence identity with isoforms of the enzyme 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase from several tissues and species. (garvan.org.au)
- Surprisingly, although actinobacillus species are more closely related to pasteurellae than to members of the family Enterobacteriaciae, LktA and LktC from A. actinomycetemcomitans shared significantly greater sequence identity with the E. coli alpha-hemolysin proteins than with the P. haemolytica leukotoxin proteins. (asm.org)
- Thus, WebScipio should be able to identify mutually exclusive spliced exons in any query sequence from any species with a very high probability. (biomedcentral.com)
- BLASTN key features are searching with short sequencing and cross-species comparison. (omictools.com)
- In this study we compared the sequences of the 16s rRNA and the intraspecies sequences were compared for each hominidae and the phylogenic trees were constructed for all the species. (scitechnol.com)
- 8 ]). The diversity of ecologies represented by members of Vibrionaceae has led to enthusiastic genome sequencing in the group, which has focused most heavily on pathogenic species (more than 31 strains of V. cholerae are available on GenBank as of 2012). (biomedcentral.com)
- Sequences are the middle 120-180 amino acid residues of the proteins. (wikipedia.org)
- Residues that are conserved across all sequences are highlighted in grey. (wikipedia.org)
- The percentage of identical residues ( percent identity ) or the percentage of residues conserved with similar physicochemical properties ( percent similarity ), e.g. leucine and isoleucine , is usually used to "quantify the homology. (wikipedia.org)
- The inverse of this relation is used to search a database for triplets of adjacent residues with secondary chemical shifts and sequence similarity which provide the best match to the query triplet of interest. (nih.gov)
- The computer program TALOS was developed to search this database for strings of residues with chemical shift and residue type homology. (nih.gov)
- If you have a template structure with 85% sequence identity to your target, the mainchain RMS error in the target model is likely to be around 0.7A for at least 95% of the residues. (bio.net)
- Background: Prediction of protein structural classes (a, b, a + b and a/b) from amino acid sequences is of great importance, as it is beneficial to study protein function, regulation and interactions. (ntu.edu.sg)
- Results: We propose a new method to predict protein structural classes on the basis of features extracted from the predicted secondary structures of proteins rather than directly from their amino acid sequences. (ntu.edu.sg)
- Conclusion: The high prediction accuracy achieved by our proposed method is attributed to the design of a comprehensive feature set on the predicted secondary structure sequences, which is capable of characterizing the sequence order information, local interactions of the secondary structural elements, and spacial arrangements of a helices and b strands. (ntu.edu.sg)
- Thus, it is a valuable method to predict protein structural classes particularly for low-homology amino acid sequences. (ntu.edu.sg)
- structural hypothesis from sequence data? (bio.net)
- We have assessed the generality and sequence specificity of this transnuclear maternal control by studying the effects of macronuclear transformation with 13 different IESs. (asm.org)
Based on sequence similarity1
- Among these, 61 were identified in M. leprae based on sequence similarity and domain architecture. (iith.ac.in)
- To detect the homology of a protein to a protein family, we utilize the feature vectors containing all pairwise similarity scores between the test protein and the proteins in the training set. (metu.edu.tr)
- Specifically, marker DNA sequences which detect either directly or indirectly. (google.com.au)
- These sequences may be used to generate DNA hybridization probes and antibodies for assays to detect a person's susceptibility to autoimmune diseases, such as IDDM and PV. (google.com.au)
- 10. The marker DNA sequence of claim 7 wherein said DNA sequence is used to detect indirectly a second DNA sequence comprising the codon at position 57 wherein said codon 57 is selected from the group consisting of codons for alanine, valine and aspartate. (google.com.au)
- Such homologies have been found by computer searches in which decapeptides in two human myelin proteins were compared with proteins of viruses known to infect humans. (sciencemag.org)
- Complete DNA sequences can be used as a platform to develop rapid epidemiologic tools to identify and trace the spread of plasmids in clinically relevant pathogens, thus facilitating a better understanding of their distribution and ability to transfer between bacteria of humans and animals. (cdc.gov)
- We tested the proposed method on three benchmark datasets in low homology and achieved the overall prediction accuracies of 82.9%, 83.1% and 81.3%, respectively. (ntu.edu.sg)
- The tool presented here, PyMod, aims to give researchers and students with no or a limited familiarity in this field, as well as more experienced users, the ability to exploit popular algorithms in sequence/structure analysis and protein structure prediction, and most importantly full customization and control over their parameters, while retaining as much as possible an ease of use and the familiarity of the PyMOL environment (Figure 1 ). (biomedcentral.com)
- This will include structure prediction using homology and ab initio protein modelling, building protein-ligand and protein-protein complexes and fitting the atomistic data to lower-resolution sets. (ncl.ac.uk)
- As with morphological and anatomical structures, sequence similarity might occur because of convergent evolution , or, as with shorter sequences, by chance, meaning that they are not homologous. (wikipedia.org)
- In biology, homology is commonly defined as any similarity between structures of organisms in different taxa that derives from similar structures in their shared ancestry. (newworldencyclopedia.org)
- In biology , homology refers to the general and quite ancient observation of similarity of form seen in the biological world of animals or plants. (wikidoc.org)
- More specifically, in evolutionary biology , homology has come to mean any similarity between characters that is due to their shared ancestry . (wikidoc.org)
- In most mammals, the X and Y chromosomes synapse and recombine along a conserved region of homology known as the pseudoautosomal region (PAR). (genetics.org)
- We report here the first comprehensive comparative NH2‐terminal sequence studies of interstitial retinolbinding protein (IRBPs) from nine mammals (including cattle) and one amphibian. (semanticscholar.org)
- The principle of homology illustrated by the adaptive radiation of the forelimb of mammals. (newworldencyclopedia.org)
- Forelimbs in mammals provide one example of homology. (wikidoc.org)
- Software.ncrna.org: Web servers for analyses of RNA sequences. (currentprotocols.com)
- Assigns every individual read sequence within a dataset taxonomically by cascading different sequence analyses with decreasing stringency of the assignments using various software applications. (omictools.com)
- The high accuracy and performance of RIEMS analyses were proven in comparison with other tools for metagenomics data analysis using simulated sequencing read datasets. (omictools.com)
- Analyses of the 44-taxon sampling based on the second, small chromosome are quite different from those based on the large chromosome, which is not surprising given the dramatically divergent nature of the small chromosome and the difficulty in postulating primary homologies. (biomedcentral.com)
- Partial homology can occur where a segment of the compared sequences has a shared origin, while the rest does not. (wikipedia.org)
- Preliminary calculations suggest that sequence homology recognition within the triplex of association is partial and that it is completed during strand exchange and product formation. (jbsdonline.com)
- Closely correlated partial sequences in DNA or protein could be similarly labeled if common ancestry is considered to be the cause. (newworldencyclopedia.org)
- One can, however, refer to partial homology where a fraction of the sequences compared (are presumed to) share descent, while the rest does not. (wikidoc.org)
- The tool is fully equipped with applications to generate search databases from GenBank or from the user's own sequence data. (nih.gov)
- Through its WWW server (http://www.mips.biochem.mpg.de/ ) MIPS permits internet access to sequence databases, homology data and to yeast genome information. (nih.gov)
- iii) The HPT (hashed position tree) data structure () developed at MIPS is a new approach for rapid sequence and pattern searching. (nih.gov)
- I hypothesize that by exploiting the sheer amount of computation power and sequencing data, it is possible to deduce information from raw sequences without supplying the underlying prior knowledge to come up with an answer. (umsystem.edu)
- Our data demonstrate that for tetanus toxin and botulinum toxin types B, C1, and E this region also has immunological homology. (asm.org)
- These data also suggest that although the native structures of tetanus and botulinum toxins have relatively few common immunological determinants, the two toxins may contain short stretches of identical or very similar amino acid sequences. (asm.org)
- Allows users to taxonomically and functionally explore and analyze large-scale microbiome sequencing data. (omictools.com)
- EB-eye), services to retrieve entry data in various data formats and to access the data in specific fields (e.g. dbfetch), and analysis tool services, for example, sequence similarity search (e.g. (psu.edu)
- In benchmarking experiments on artificial data we observe that the inclusion of thermodynamic stability is helpful, albeit only in a regime of extremely low sequence information in the query. (biomedcentral.com)
- Six published repetitive immunogenic amino acid sequences from the circumsporozoite (CS) antigen, ring-infected erythrocyte surface antigen (RESA), soluble (S) antigen, and falciparum interspersed repetitive antigen (FIRA) of P. falciparum, and the CS protein of P. vivax, were analyzed by computer. (ajtmh.org)
- In the database, 29 matches were found for human proteins and 26 matches were found for human viruses with the 6 antigen sequences. (ajtmh.org)
- Sequence similarity searching, typically with BLAST (units 3.3, 3.4), is the most widely used, and most reliable, strategy for characterizing newly determined sequences. (merlot.org)
- Blast this sequence against all of PDB Archive. (rcsb.org)
- But it is unclear to me why do you want to assign a name from a blast search to your sequences. (biostars.org)
- What Is A Good Web Front End For (Blast) Homology Search? (biostars.org)
- One fairly common task is to make some sequences available for BLAST search over the web. (biostars.org)
- PSI-]BLAST, ClustalW, MUSCLE, CEalign and MODELLER) has been developed, to show how the integration of the individual steps required for homology modeling and sequence/structure analysis within the PyMOL framework can hugely simplify these tasks. (biomedcentral.com)
- It finally compares metagenomic reads against this precomputed marker catalog using nucleotide BLAST searches in order to provide clade abundances for one or more sequenced metagenomes. (omictools.com)
- Once the assemblies are done, identify the chloroplast contigs by BLAST homology searches. (ukgoldenessays.com)
- Position rRNAs by using BLAST homology searches in pairwise mode (0). (ukgoldenessays.com)
- Thus, we made a Ruby script, mafftE.rb, which aligns the input sequences together with their close homo-logues collected from SwissProt using NCBI-BLAST. (psu.edu)
- Current homology search tools for structured RNAs are either based entirely on sequence similarity (such as blast or hmmer ) or combine sequence and secondary structure. (biomedcentral.com)
- A central function of RecA protein during homologous recombination is to promote sequence recognition and strand exchange between a stretched and unwound single-stranded DNA, to which it is complexed, and a duplex DNA. (jbsdonline.com)
- Recombination between adenovirus type 12 DNA and a hamster preinsertion sequence in a cell-free system. (uni-muenchen.de)
- We have previously described a cell-free recombination system derived from hamster cell nuclear extracts in which the in vitro recombination between a hamster preinsertion sequence, the cloned 1768 base-pair p7 fragment, and adenovirus type 12 (Ad12) DNA has been demonstrated. (uni-muenchen.de)
- By using these protein subfractions, in vitro recombinants have been generated between the p7 preinsertion sequence and the 60 to 70 map unit fragment of Ad12 DNA, which has previously shown high recombination frequency. (uni-muenchen.de)
- These sequences participate in the recombination reactions catalyzed by the same column fractions in the shoulder of the absorbancy profile. (uni-muenchen.de)
- This is not to be confused with conservation in amino acid sequences, where the amino acid at a specific position has been substituted with a different one that has functionally equivalent physicochemical properties. (wikipedia.org)
- This is not to be confused with conservation in amino acid sequences in which the amino acid at a specific position has changed but the physio-chemical properties of the amino acid remain unchanged. (wikidoc.org)
- The identification of similar sequences in this report is based on clustering as described here . (rcsb.org)
- In the table for each entity, view a list of similar sequences by selecting the link associated with the percentage cutoff. (rcsb.org)
- Users can select an optimization according to: (i) highly similar sequences, (ii) more dissimilar sequences or (iii) somewhat similar sequences. (omictools.com)