• In the absence of an affordable and capable technology to generate and assemble a conifer genome, previous investigations have relied on other techniques to generate sequence for basic and applied research in pine genetics. (genetics.org)
  • Alignments of multiple sequences are used to indicate which regions of each sequence are homologous. (wikipedia.org)
  • These include the default T-Coffee mode for protein and nucleic acid sequences, the M-Coffee mode that allows combining the output of any other aligners, and template-based modes of T-Coffee that deliver high accuracy alignments while using structural or homology derived templates. (nih.gov)
  • Multiple sequences alignments (MSAs) provide essential information on the evolution of protein families. (pnas.org)
  • Because three or more sequences of biologically relevant length can be difficult and are almost always time-consuming to align by hand, computational algorithms are used to produce and analyze the alignments. (wikipedia.org)
  • Multiple sequence alignments can be helpful in many circumstances like detecting historical and familial relations between sequences of proteins or amino acids and determining certain structures or locations on sequences. (wikipedia.org)
  • Therefore it make sense to construct an algorithm to assist in repetitive calculations of multiple sequence alignments. (wikipedia.org)
  • A general approach when calculating multiple sequence alignments is to use graphs to identify all of the different alignments. (wikipedia.org)
  • 227] Pritha Ghosh, Teerna Bhattacharya, Oommen K. Mathew and R. Sowdhamini (2019) PASS2 version 6 a database of structure based sequence alignments of protein domain superfamilies in accordance with SCOPe. (ncbs.res.in)
  • CS-BLAST greatly improves alignment quality over the entire range of sequence identities and especially for difficult alignments in comparison to regular BLAST and PSI-BLAST. (wikipedia.org)
  • S4: structure-based sequence alignments of SCOP superfamilies. (vldb.org)
  • Sequence alignments revealed conserved motifs and suggested that rotavirus and orbivirus capping enzymes contain a variable N-terminal domain, a central guanine-N7-methyltransferase domain that contains an additional inserted domain, and a C-terminal guanylyltransferase and RNA 5′-triphosphatase domain. (asm.org)
  • In this study, we used sequence- and structure-based alignments with related proteins to predict the structure of VP3 and identify enzymatic domains and active sites therein. (asm.org)
  • Homology among DNA, RNA, or proteins is typically inferred from their nucleotide or amino acid sequence similarity. (wikipedia.org)
  • Significant similarity is strong evidence that two sequences are related by evolutionary changes from a common ancestral sequence. (wikipedia.org)
  • The term "percent homology" is often used to mean "sequence similarity. (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)
  • Based on the definition of homology specified above this terminology is incorrect since sequence similarity is the observation, homology is the conclusion. (wikipedia.org)
  • 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)
  • Significant sequence similarity and shared functional domains indicate that these two genes are orthologous genes, [4] inherited from the shared ancestor . (wikipedia.org)
  • The cDNA is assumed to encode alpha-1-antitrypsin on the basis of its sequence similarity to the corresponding cDNAs for human, baboon, rat, mouse, sheep and cow. (biomedsearch.com)
  • C.B. Lawrence , Use of Homology Domains in Sequence Similarity Detection. (elsevier.com)
  • HorA web server to infer homology between proteins using sequence and structural similarity. (nih.gov)
  • 1. An isolated nucleic acid encoding an endothelial estrogen regulated gene-7 protein that has (i) an amino acid sequence which has at least about 95% sequence similarity with SEQ ID NO: 2 and (ii) lysyl oxidase activity. (google.com)
  • Cytosine methyltransferases can also be categorized on the basis of enzyme structure and similarity of conserved amino acid motifs. (genetics.org)
  • Please call it sequence SIMILARITY In a search you may find many sequence similarities but only few of the matches may represent homologies. (bio.net)
  • Homologous proteins (proteins who have common ancestry) are inferred from their sequence similarity. (wikipedia.org)
  • A FIGURE NEEDS TO GO HERE THIS IS THE CAPTION) "Sequence search/alignment algorithms find the path that maximizes the sum of similarity scores (color-coded blue to red). (wikipedia.org)
  • Despite the pronounced similarity of the three restriction-modification systems, the flanking sequences in Proteus and Salmonella are completely different. (asm.org)
  • Homology -- Similarity of nucleotide or amino acid sequences in nucleic acids, peptides, or proteins. (nih.gov)
  • The deduced amino acid sequence of APO-1 showed sequence identity with the Fas antigen, a cysteine-rich transmembrane protein of 335 amino acids with significant similarity to the members of the tumor necrosis factor/nerve growth factor receptor superfamily. (uni-regensburg.de)
  • Bet v 1 has been identified as existing in three subfamilies, based on the sequence similarity. (intechopen.com)
  • 1987) Homology in proteins and nucleic acids: A terminology muddle and a way out of it. (bio.net)
  • PDBsum more: new summaries and analyses of the known 3D structures of proteins and nucleic acids. (vldb.org)
  • The structural gene entC3, which encodes staphylococcal enterotoxin C3 was cloned from the genome of Staphylococcus aureus FRI-913 and sequenced. (nih.gov)
  • One sequence, Ta17, is located in the mitochondrial genome. (harvard.edu)
  • The paucity of retrotransposons and the small genome size of A. thaliana support the hypothesis that most repetitive sequences have been lost from the genome and that mechanisms may exist to prevent amplification of extant element families. (harvard.edu)
  • In addition, flat file access to the FASTA sequences of the genome and transcriptome, annotations, and gff3 files are available through the database FTP site ( http://loblolly.ucdavis.edu/bipod/ftp/Genome_Data/genome/pinerefseq/Pita/ ). (genetics.org)
  • In this study, we present the annotation of the first whole-genome shotgun assembly of loblolly pine ( Pinus taeda L.), which comprises 20.1 Gb of sequence. (genetics.org)
  • To date, the only complete bacterial genome sequences lacking candidate RM systems are from the obligate intracellular parasites Chlamydia and Rickettsia . (asm.org)
  • With the advent of the post genome era and the development of sequencing technology, how to find all forms of miRNAs from millions of reads has become one of the challenging topics in bioinformatics. (springer.com)
  • Mercator: a fast and simple web server for genome scale functional annotation of plant sequence data. (mpg.de)
  • Many eukaryotes preferentially use the NHEJ pathway to repair a DSB, and exogenous targeting DNA can be integrated anywhere into the genome independent of DNA sequence homology ( 27 ). (asm.org)
  • We have developed a new method for the identification of domains in unassigned regions through indirect connections and scaled up its application to the analysis of 434 unassigned regions in 726 protein sequences of Mycoplasma gallisepticum genome. (pubmedcentralcanada.ca)
  • We could establish 71 new domain relationships and probable 63 putative new domain families through intermediate sequences in the unassigned regions, which importantly represent an overall 10% increase in PfamA domain annotation over the direct assignment in this genome. (pubmedcentralcanada.ca)
  • This pathogen has a small genome with 726 proteins [ 8 ], but only 498 protein sequences have known Pfam hits with 46% residue coverage [ 9 ]. (pubmedcentralcanada.ca)
  • The gap in the annotation of this genome emphasizes the need for further exploration for other methods for domain assignment from sequence. (pubmedcentralcanada.ca)
  • of these 44, 10 are homologous to entries in the complete K-12 genome sequence, 4 are nearly identical to the sequences of E. coli J96 encoding the HlyA hemolysin, 11 encode P fimbriae, and 19 show no homology to J96 or K-12 entries. (asm.org)
  • 30-kb) blocks of DNA inserted within or near tRNA genes ( 12 , 33 , 39 ), contain direct repeats and insertion sequences, have a GC content that differs from that of the rest of the genome, and encode defined virulence determinants ( 3 , 19 , 26 ). (asm.org)
  • Sequence comparison of mitochondrial tRNA genes and origin of light strand replication in Bos taurus. (biomedsearch.com)
  • The outbreak strains showed identical nucleotide sequences in genes encoding three rotavirus proteins, VP7, VP8, and NSP4, but they were distinct from G9P[8] strains isolated in previous years. (cdc.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)
  • Comparative analysis of the sequence and structure of two Drosophila melanogaster genes encoding vitelline membrane proteins. (nextbio.com)
  • 2000 ) identified maize ( Zmet3 ) and Arabidopsis ( DRM ) genes encoding proteins closely related to Dnmt3 methyltransferases but containing a novel arrangement of the eight diagnostic methyltransferase amino acid motifs. (genetics.org)
  • Such genes significantly affected the metabolism of lipid, cellular ketone, organic acid, and carboxylic acids. (nih.gov)
  • Compilation of tRNA sequences and sequences of tRNA genes. (vldb.org)
  • Consensus sequences noted in many other eukaryotic genes, as well as histone-specific consensus sequences, have been identified. (springer.com)
  • An unusual feature of the spacer region between the H4 and H2B genes is the presence of a duplicated sequence 87 bp in length. (springer.com)
  • Connor W, States JC, Mezquita J, Dixon GH (1984b) Organization and nucleotide sequence of rainbow trout histone H2A and H3 genes. (springer.com)
  • Antisense peptide nucleic acids (PNAs) exhibit growth inhibitory effects on bacteria by inhibiting the expression of essential genes and could be promising therapeutic agents for treating bacterial infections. (scirp.org)
  • The 57,988-bp stretch of DNA has characteristics which define PAIs, including a size greater than 30 kb, the presence of insertion sequences, distinct segmentation of K-12 and J96 origin, GC content (42.9%) different from that of total genomic DNA (50.8%), and the presence of virulence genes ( hly and pap ). (asm.org)
  • Comparison of the bacterial 16S rRNA gene sequence has emerged as a preferred genetic technique. (asm.org)
  • Problems remain in that the sequences in some databases are not accurate, there is no consensus quantitative definition of genus or species based on 16S rRNA gene sequence data, the proliferation of species names based on minimal genetic and phenotypic differences raises communication difficulties, and microheterogeneity in 16S rRNA gene sequence within a species is common. (asm.org)
  • DNA, or deoxyribonucleic acid -- The primary genetic material of all cellular organisms and the DNA viruses. (nih.gov)
  • RNA, viral -- Ribonucleic acid that makes up the genetic material of viruses. (nih.gov)
  • Several lines of experimental evidence argue in favor of a dominant role of positive selection for amino acid changes in driving the pattern of HVR1 genetic diversification ( 1 , 2 ). (jimmunol.org)
  • R. Staden , Searching for Patterns in Protein and Nucleic Acid Sequences. (elsevier.com)
  • Visual depictions of the alignment as in the image at right illustrate mutation events such as point mutations (single amino acid or nucleotide changes) that appear as differing characters in a single alignment column, and insertion or deletion mutations ( indels or gaps) that appear as hyphens in one or more of the sequences in the alignment. (wikipedia.org)
  • CS-BLAST (Context-Specific BLAST) is a tool that searches a protein sequence that extends BLAST (Basic Local Alignment Search Tool), using context-specific mutation probabilities. (wikipedia.org)
  • It was possible to use this CRISPR system to create a single conserved amino acid substitution (A189G) mutation for both alleles of RAD51 , a DNA recombinase involved in homology-directed repair. (asm.org)
  • Endoproteinase-cleaved peptides of the APO-1 protein were subjected to amino acid sequencing, and corresponding oligonucleotides were used to identify a full-length APO-1 cDNA clone from an SKW6.4 cDNA library. (uni-regensburg.de)
  • Peptides containing this sequence motif exhibited monocyte activating capacity similar to the autocrine stimulatory capacity of hTNF alpha itself. (uni-regensburg.de)
  • A high number of specific clones was obtained after immunization with a pool of nine mimotopes, and the resulting mAbs were shown to recognize several 16- and 27-mer peptides derived from natural HVR1 sequences isolated from patients with acute and chronic HCV infection, suggesting that HVR1 mimotopes were efficient antigenic and immunogenic mimics of naturally occurring HCV variants. (jimmunol.org)
  • Prospective studies of serological responses to synthetic oligopeptides derived from HVR1 sequences of patients with acute and chronic HCV infection showed apparently extensive serological cross-reactivity for unrelated HVR1 peptides in the majority of the patients ( 3 , 4 , 5 , 6 , 7 , 8 , 9 ). (jimmunol.org)
  • These three available template modes are Expresso for the alignment of protein with a known 3D-Structure, R-Coffee to align RNA sequences with conserved secondary structures and PSI-Coffee to accurately align distantly related sequences using homology extension. (nih.gov)
  • H.M. Martinez , Detecting Pseudoknots and Other Local Base-Pairing Structures in RNA Sequences. (elsevier.com)
  • Notwithstanding, the information currently available on protein sequences, structures, functions, and interactions opens the door to performing more comprehensive studies of the relationships between family organization and functional divergence ( 17 ). (pnas.org)
  • Multiple sequence alignment is often used to assess sequence conservation of protein domains , tertiary and secondary structures, and even individual amino acids or nucleotides. (wikipedia.org)
  • Homology is the relationship between biological structures or sequences derived from a common ancestor. (wikipedia.org)
  • The structures and structural coordinates are useful in structural homology deduction, in developing and screening agents that affect the activity of eukaryotic RNA polymerase, and in designing modified forms of eukaryotic RNA polymerase. (freepatentsonline.com)
  • The high prediction accuracy achieved by our proposed method is attributed to the design of a comprehensive feature set on the sequences and secondary structures, which are capable of characterizing the sequence evolution information and sequence-order information, and global and local information of pre-microRNAs secondary structures. (springer.com)
  • On the other hand, as mature miRNAs are very short, the traditional feature engineering approaches [ 4 ] are usually failed to extract effective features from their sequences and structures. (springer.com)
  • The search process is a typical alignment problem of sequences and structures. (springer.com)
  • of fast alignment algorithms construct auxiliary data structures, called indices, for the read sequences or the reference sequence, or sometimes both. (psu.edu)
  • MARs are typically AT-rich elements that contain consensus cleavage sites for topoisomerase II, and they may contain one or more loosely defined short sequence motifs, but, in general, their structures are not highly homologous. (asm.org)
  • Enriching the annotation of Mycobacterium tuberculosis H37Rv proteome using remote homology detection approaches: insights into structure and function. (ncbs.res.in)
  • DDBJ in collaboration with mass-sequencing teams on annotation. (vldb.org)
  • geneid - Gene prediction tool, it can also introduce homology and annotation evidences and produce a reannotation of a genomic sequence. (bioinformatics.org)
  • 2. SWISS-PROT - a curated protein sequence database which strives to provide a high level of annotation. (tau.ac.il)
  • 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)
  • 2016) is a bioinformatics tool for estimating the evolutionary conservation of amino/nucleic acid positions in a protein/DNA/RNA molecule based on the phylogenetic relations between homologous sequences. (tau.ac.il)
  • A multiple sequence alignment (MSA) of the homologous sequences is constructed using MAFFT (default), PRANK, T-COFFEE, MUSCLE or CLUSTALW. (tau.ac.il)
  • Biegert and Söding, 2009) heuristic algorithm with default parameters to collect homologous sequences of a single polypeptide chain of known 3D-structure. (tau.ac.il)
  • A sequence alignment of mammalian histone proteins. (wikipedia.org)
  • T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension. (nih.gov)
  • This article introduces a new interface for T-Coffee, a consistency-based multiple sequence alignment program. (nih.gov)
  • The top part is a color-coded alignment where sequences in red correspond to alignment portions with a strong support in the primary library. (nih.gov)
  • M.S. Waterman and R. Jones , Consensus Methods for DNA and Protein Sequence Alignment. (elsevier.com)
  • D.-F. Feng and R.F. Doolittle , Progressive Alignment and Phylogenetic Tree Construction of Protein Sequences. (elsevier.com)
  • G.J. Barton , Protein Multiple Sequence Alignment and Flexible Pattern Matching. (elsevier.com)
  • G.M. Landau, U. Vishkin, and R. Nussinov , Fast Alignment of DNA and Protein Sequences. (elsevier.com)
  • First 90 positions of a protein multiple sequence alignment of instances of the acidic ribosomal protein P0 (L10E) from several organisms. (wikipedia.org)
  • A multiple sequence alignment ( MSA ) is a sequence alignment of three or more biological sequences , generally protein , DNA , or RNA . (wikipedia.org)
  • Multiple sequence alignment also refers to the process of aligning such a sequence set. (wikipedia.org)
  • Most multiple sequence alignment programs use heuristic methods rather than global optimization because identifying the optimal alignment between more than a few sequences of moderate length is prohibitively computationally expensive. (wikipedia.org)
  • When choosing traces for a set of sequences it is necessary to choose a trace with a maximum weight to get the best alignment of the sequences. (wikipedia.org)
  • The figure illustrates the sequence to sequence and profile to sequence equivalence with the alignment matrix. (wikipedia.org)
  • A DIFFERENT GRAPH NEEDS TO GO HERE) CS-BLAST offers improved sensitivity and alignment quality in sequence comparison. (wikipedia.org)
  • This page shows the publications Kiran Musunuru has written about Sequence Alignment. (harvard.edu)
  • A central challenge to the analysis of this data is sequence alignment, whereby sequence reads must be compared to a reference. (psu.edu)
  • We also consider future development of alignment algorithms with respect to emerging long sequence reads and the prospect of cloud computing. (psu.edu)
  • The protein sequence alignment was performed by T-Coffee method. (hindawi.com)
  • In the current study, we used sequence alignment and homology modeling to identify features common to nonturreted Reoviridae capping enzymes and to predict the domain organization, structure, and active sites of rotavirus VP3. (asm.org)
  • 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 new server benefits from recent improvements of the T-Coffee algorithm and can align up to 150 sequences as long as 10,000 residues and is available from both http://www.tcoffee.org and its main mirror http://tcoffee.crg.cat. (nih.gov)
  • Thus, the first 27 residues of the toxin precursor comprise the signal peptide, and the mature toxin contains 239 amino acids with a molecular weight of 27,563 daltons. (nih.gov)
  • Enterotoxin C3 differs from enterotoxin C2 by four amino acids and from enterotoxin C1 by nine residues. (nih.gov)
  • The 167 C-terminal residues of the three toxins are identical, except for one conservative amino acid substitution in enterotoxin C3. (nih.gov)
  • 1985) determined that human plasma Hx consists of a single polypeptide chain of 439 amino acids residues with six intrachain disulfide bridges and has a molecular mass of approximately 63 kD. (wikidoc.org)
  • The complete sequence of a beta-mannanase gene from an anaerobic extreme thermophile was determined, and it shows that the expressed protein consists of two catalytic domains and two binding domains separated by spacer regions rich in proline and threonine residues. (asm.org)
  • 1. UniRef90 - consists of cluster sequences and sub-fragments with 11 or more residues that have at least 90% sequence identity with each other (from any organism) into a single UniRef entry, displaying the sequence of a representative. (tau.ac.il)
  • The hypervariable region 1 (HVR1) of the E2 protein of hepatitis C virus (HCV) is a highly heterogeneous sequence that is promiscuously recognized by human sera via binding to amino acid residues with conserved physicochemical properties. (jimmunol.org)
  • 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)
  • Phylogenetic analyses indicated that the A. thaliana sequences are more closely related to each other than to elements from other organisms, consistent with the vertical evolution of these sequences over most of their evolutionary history. (harvard.edu)
  • From the resulting MSA, sequence homology can be inferred and phylogenetic analysis can be conducted to assess the sequences' shared evolutionary origins. (wikipedia.org)
  • Universal phylogenetic tree based on the 16S rRNA gene sequence comparisons. (asm.org)
  • This involves that the term "percent homology" is a misnomer. (wikipedia.org)
  • Her research focuses on developing hydrogel-based platforms and biosensors for the detection and sensing of circulating nucleic acid biomarkers from liquid biopsy. (selectbiosciences.com)
  • Antisense/antigene therapy using peptide nucleic acids (PNAs) has the potential to help control MDR bacterial infections. (scirp.org)
  • The high degree of homology between the 4q35 and the 10q26 D4F104S1 region is thought to have been responsible for interchromosomal exchanges between these two regions. (barnardhealth.us)
  • Homologous sequence regions are also called conserved . (wikipedia.org)
  • R. Staden , Finding Protein Coding Regions in Genomic Sequences. (elsevier.com)
  • Several of the amino acid substitutions on the VP7 and NSP4 proteins were identified in regions known to influence function and may have contributed to the emergence and increased dominance of the outbreak strains. (cdc.gov)
  • UTRdb and UTRsite: a collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs. (vldb.org)
  • Here, the bioinformatic algorithms were applied for known Bet v 1 homologous nucleic acids sequences to find homology and conserved regions. (intechopen.com)
  • The positions in MSAs can be interpreted in terms of the amino acid changes allowed or disallowed during evolution, and therefore useful information at the residue level can be inferred from them ( 4 ). (pnas.org)
  • Smith JB (2001) Peptide sequencing by Edman degradation. (springer.com)
  • Synthetic insertion signal sequences enhance MHC class I presentation of a peptide from the melanoma antigen MART-1, 2000, Eur. (patentgenius.com)
  • Due to high evolutionary divergence, it is not always possible to identify distantly related protein domains by sequence search techniques. (pubmedcentralcanada.ca)
  • A polymerase chain reaction assay was developed based on conserved amino acid sequences shared between the Ta11-1 reverse transcriptase and those of non-LTR retrotransposons from other species. (harvard.edu)
  • 4. A chimeric gene capable of transforming a plant cell of an oil-producing species comprising a nucleic acid fragment of Claim 1 operably linked to suitable regulatory sequences resulting in overexpression of said soybean seed stearoyl-ACP desaturase in the plastid of said plant cell. (epo.org)
  • These methods mainly utilize the conservation characteristics of miRNAs and their precursor sequences in multiple species to search for the conserved sequences in the intergenic region. (springer.com)
  • Genomic sequences of PR proteins of two different fruit species, which allergens belong to PR proteins of the same type as Bet v 1, were selected to design degenerate primers. (intechopen.com)
  • Subsequently, screening of the presence of Bet v 1 conserved genomic sequence was performed in 45 clinically relevant plant species. (intechopen.com)
  • Sequence conservation and homology modeling suggested that the insertion in the guanine-N7-methyltransferase domain is a ribose-2′- O -methyltransferase domain for most rotavirus species. (asm.org)
  • PA-GOSUB: a searchable database of model organism protein sequences with their predicted Gene Ontology molecular function and subcellular localization. (vldb.org)
  • We have developed methodologies for the molecular identification of rotavirus strains based on VP7 gene segment sequence. (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)
  • Such hybridization is highly specific and, therefore, enables identification of different types and sequences of DNA and RNA. (nih.gov)
  • MSRV was found to be related to the endogenous retroviral sequence ERV-9 ( 26 ), and Southern blot analysis with an MSRV pol probe showed hybridization with a multicopy endogenous family ( 40 ). (pubmedcentralcanada.ca)
  • Determination and augmentation of RNA sequence specificity of the Nova K-homology domains. (harvard.edu)
  • The structure of protein families is shaped by the sequence divergence accumulated as a consequence of speciation, gene duplication, and deletion events, as well as by the evolutionary selective pressure exerted on each protein in accordance with the corresponding 3D structure and the specific function performed ( 1 , 2 ). (pnas.org)
  • In many cases, the input set of query sequences are assumed to have an evolutionary relationship by which they share a linkage and are descended from a common ancestor. (wikipedia.org)
  • Clerc RG, Bucher P, Strub K, Birnstiel ML (1983) Transcription of a cloned Xenopus laevis H4 histone gene in the homologous frog oocyte system depends on an evolutionary conserved sequence motif in the −50 region. (springer.com)
  • The degree to which an amino (or nucleic) acid position is evolutionarily conserved (i.e., its evolutionary rate) is strongly dependent on its structural and functional importance. (tau.ac.il)
  • Centromeric repeat arrays hypomethylated in met1-1 mutants are partially remethylated when introduced into a wild-type background, in contrast to genomic sequences hypomethylated in ddm1 mutants. (genetics.org)
  • The protein sequence of H4, as determined from the nucleic acid sequence, is the same as that derived for other vertebrate H4 proteins, although comparison of nucleotide sequences shows a great deal of sequence divergence, especially in the third base position. (springer.com)
  • However, these methods can only find highly homologous miRNAs with known miRNA sequences and require a large amount of computational resource for whole genomes. (springer.com)
  • The homologous recombination pathways repair a DSB using mechanisms that recognize highly homologous DNA sequences, while the nonhomologous end-joining (NHEJ) pathway does not rely on DNA sequence homology. (asm.org)
  • VT1 is highly homologous to Stx of Shigella dysenteriae type I. VT2 shares approximately 55% amino acid homology with VT1 but is relatively more heterogeneous. (asm.org)
  • DoOP: Databases of Orthologous Promoters, collections of clusters of orthologous upstream sequences from chordates and plants. (vldb.org)
  • Computer analysis of the uvrD coding sequence has indicated that it contains seven conserved motifs that are shared by a superfamily of proteins involved in DNA metabolism ( 16 ). (asm.org)
  • Motifs IA, IB, and II, previously identified as Walker A and Walker B sequences, respectively, are conserved segments found in many nucleoside triphosphate-binding proteins and all helicases characterized to date ( 14 , 15 , 46 ). (asm.org)
  • Combining expression and sequence data: searching for motifs in expression clusters (Tavazoie), linear contribution of motifs to expression levels (Bussemaker), combinations of motifs (Pilpel). (indiana.edu)
  • A cDNA clone encoding the complete coding sequence for porcine alpha-1-antitrypsin (or alpha 1-protease inhibitor, PI) was isolated and its DNA sequence determined. (biomedsearch.com)
  • 4. The isolated nucleic acid of claim 1 , which is a cDNA. (google.com)
  • 6. The isolated nucleic acid of claim 5 , which is a cDNA. (google.com)
  • 8. The isolated nucleic acid of claim 7 , which is a cDNA. (google.com)
  • The complete cDNA sequence and expression of the first major allergenic protein of Malassezia furfur , Mal f 1," European Journal of Biochemistry , vol. 246, no. 1, pp. 181-185, 1997. (hindawi.com)
  • DNA sequence analysis near the Arabidopsis thaliana ABI3 gene revealed the presence of a non-LTR retrotransposon insertion that we have designated Ta11-1. (harvard.edu)
  • In addition, computer-assisted analysis revealed a potential ATP -binding domain in the predicted UL37 amino acid sequence. (curehunter.com)
  • Sequence analysis demonstrated 100% homology with a rabies virus variant associated with the silver-haired bat ( Lasionycteris noctivagans ). (cdc.gov)
  • 16S rRNA gene sequence analysis can better identify poorly described, rarely isolated, or phenotypically aberrant strains, can be routinely used for identification of mycobacteria, and can lead to the recognition of novel pathogens and noncultured bacteria. (asm.org)
  • Despite its accuracy, 16S rRNA gene sequence analysis lacks widespread use beyond the large and reference laboratories because of technical and cost considerations. (asm.org)
  • The goal of this review is to describe not only the mechanism and limits of bacterial 16S rRNA gene sequence analysis but also the impact and potential contribution that the 16S rRNA gene sequence analysis can make to the understanding of clinical microbiology and infectious diseases. (asm.org)
  • Computer-assisted analysis of the internal homology in amino acid sequence suggested duplication of an ancestral gene thus indicating that Hx consists of two similar halves. (wikidoc.org)
  • In this report, we provide an analysis of the nucleotide sequence for a 57,988-bp region. (asm.org)
  • Further examination of samples typed by these methods, such as by sequence analysis, is usually required to further characterize diversity within serotypes. (asm.org)
  • Bioinformatic analysis predicts a target binding sequence for miR-144 at the 32-UTR of meis1 . (zfin.org)
  • 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)
  • Smyth, V.A., Higgins, D.G., and Kennedy, B.N. (2011) mab21l2 transgenics reveal novel expression patterns of mab21l1 and mab21l2, and conserved promoter regulation without sequence conservation. (zfin.org)
  • Two organisms that are very closely related are likely to display very similar DNA sequences between two orthologs. (wikipedia.org)
  • Due to the rapid development of "-omics" technology, such as DNA microarrays [ 1 ] and next-generation sequencing (NGS) [ 2 , 3 ], scientists are now able to quantify large numbers of transcripts from organisms simultaneously. (biomedcentral.com)
  • This is calculated with the fraction: (pairs correctly aligned)/(pairs aligned) The graph is the benchmark Biegert and Söding used to evaluate homology detection. (wikipedia.org)
  • NrichD database: sequence databases enriched with computationally designed protein-like sequences aid in remote homology detection. (ncbs.res.in)
  • Identification of domains at the sequence level depends on the detection of global and local sequence similarities between a given query sequence and domain sequences found in databases such as Pfam[ 5 ]. (pubmedcentralcanada.ca)
  • however, their naturally low abundance, short length and high sequence homology represent a major challenge for quantitative and specific detection. (selectbiosciences.com)
  • Liquid chromatography coupled with mass spectrometric detection is one of the major technologies used for protein sequencing, identification, and quantification. (springer.com)
  • 2. The isolated nucleic acid of claim 1 , wherein the endothelial estrogen regulated gene-7 protein comprises four scavenger receptor cysteine rich (SRCR) domains having an amino acid sequence at least about 95% identical to the amino acid sequences of SEQ ID NOs: 3, 4, 5, and 6. (google.com)
  • 1. A vector comprising a nucleic acid molecule encoding the SV40 early region tsA58 mutant operably linked to a rat PF4 promoter. (google.com)
  • The DNA construct comprises a mammalian metallothionein gene promoter sequence fused to the mammalian hormone sequence of interest. (google.com)
  • Conversely, an organism that is further removed evolutionarily from another organism is likely to display a greater divergence in the sequence of the orthologs being studied. (wikipedia.org)
  • However, most of them mainly focus on secondary structure information of pre-microRNAs, while ignoring sequence-order information and sequence evolution information. (springer.com)
  • We use new features for the machine learning algorithms to improve the classification performance by characterizing both sequence order evolution information and secondary structure graphs. (springer.com)
  • These sequences have a better secondary structure of stem ring. (springer.com)
  • 1991 ) Max: a helix-loop-helix zipper protein that forms a sequence-specific DNA-binding complex with Myc. (biologists.org)
  • 1991 ) Nuclear targeting sequences- a consensus? (biologists.org)
  • 22. An isolated oligonucleotide primer or probe of 50-100 nucleotides, wherein said oligonucleotide comprises at least 20 consecutive nucleotides of SEQ ID NO: 1 and hybridizes under highly stringent conditions of 0.2 SSC at 68 C. and a washing condition of 50% formamide, 4 SSC at 42 C. with a nucleic acid having the nucleotide sequence of SEQ ID NO: 1. (google.com)
  • In order to have a homologous relationship, the sum of scores over all the aligned pairs of amino acids or nucleotides must be sufficiently high [2]. (wikipedia.org)
  • Similarities between amino acids or nucleotides are quantified in these substitution matrices. (wikipedia.org)
  • 1. An isolated nucleic acid fragment comprising a nucleotide sequence encoding the soybean seed stearoyl-ACP desaturase corresponding to the nucleotides 70 to 1245 in SEQ ID NO: 1, or any soybean nucleic acid fragment substantially homologous therewith encoding a functional stearoyl-ACP desaturase with the exception of a nucleic acid fragment having the sequence disclosed in Figure 2 of WO 91/13972. (epo.org)
  • Anticodon -- A sequence of three adjacent nucleotides in tRNA that binds to a complementary codon in mRNA and designates a specific amino acid during protein synthesis. (nih.gov)
  • Codon -- A sequence of three RNA or DNA nucleotides that specifies, i.e., codes for, either an amino acid or the termination of translation. (nih.gov)
  • To examine the factors governing the generation of DNA sequence rearrangements in mammalian somatic cells, we have cloned and sequenced novel junctions produced by six spontaneous deletion mutations at the aprt locus of Chinese hamster ovary cells. (nih.gov)
  • The Trypanosoma cruzi nucleic acid binding protein Tc38 presents changes in the intramitochondrial distribution during the cell cycle. (ebscohost.com)
  • The 5′ and 3′ ends of each repeat are complementary, and each repeat contains smaller repeated sequences internally, as well as a possible cruciform structure. (springer.com)
  • Cloning and sequencing of cDNAs corresponding to mite major allergen Der fll. (patentgenius.com)
  • The SBASE domain sequence resource, release 12: prediction of protein domain-architecture using support vector machines. (vldb.org)
  • T. Gojobori, E.N. Moriyama, and M. Kimura , Statistical Methods for Estimating Sequence Divergence. (elsevier.com)
  • Production of transgenic mammals involves the insertion of novel nucleic acid sequences into one or more chromosomes of the mammal. (google.com)
  • In vertebrate cells, the elimination of DSBs with minimal nucleotide sequence change involves the spatiotemporal orchestration of an apparently endless number of proteins ranging, according to their action, from the nucleotide level to nucleosome organization and chromosome architecture. (wikipathways.org)
  • W.R. Taylor , Hierarchical Method to Align Large Numbers of Biological Sequences. (elsevier.com)