Sequence Deletion: Deletion of sequences of nucleic acids from the genetic material of an individual.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.Base Sequence: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.Gene Deletion: A genetic rearrangement through loss of segments of DNA or RNA, bringing sequences which are normally separated into close proximity. This deletion may be detected using cytogenetic techniques and can also be inferred from the phenotype, indicating a deletion at one specific locus.Chromosome Deletion: Actual loss of portion of a chromosome.Sequence Analysis, DNA: A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.Genomics: The systematic study of the complete DNA sequences (GENOME) of organisms.Amino Acid Sequence: The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION.Genome: The genetic complement of an organism, including all of its GENES, as represented in its DNA, or in some cases, its RNA.Phylogeny: The relationships of groups of organisms as reflected by their genetic makeup.Genome, Viral: The complete genetic complement contained in a DNA or RNA molecule in a virus.Sequence Alignment: 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.Chromosome Mapping: Any method used for determining the location of and relative distances between genes on a chromosome.Cloning, Molecular: The insertion of recombinant DNA molecules from prokaryotic and/or eukaryotic sources into a replicating vehicle, such as a plasmid or virus vector, and the introduction of the resultant hybrid molecules into recipient cells without altering the viability of those cells.Exons: The parts of a transcript of a split GENE remaining after the INTRONS are removed. They are spliced together to become a MESSENGER RNA or other functional RNA.Genome, Bacterial: The genetic complement of a BACTERIA as represented in its DNA.Sequence Homology, Nucleic Acid: The sequential correspondence of nucleotides in one nucleic acid molecule with those of another nucleic acid molecule. Sequence homology is an indication of the genetic relatedness of different organisms and gene function.Genomic Library: A form of GENE LIBRARY containing the complete DNA sequences present in the genome of a given organism. It contrasts with a cDNA library which contains only sequences utilized in protein coding (lacking introns).Evolution, Molecular: The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.Genome, Human: The complete genetic complement contained in the DNA of a set of CHROMOSOMES in a HUMAN. The length of the human genome is about 3 billion base pairs.Introns: Sequences of DNA in the genes that are located between the EXONS. They are transcribed along with the exons but are removed from the primary gene transcript by RNA SPLICING to leave mature RNA. Some introns code for separate genes.Mutation: Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations.Open Reading Frames: A sequence of successive nucleotide triplets that are read as CODONS specifying AMINO ACIDS and begin with an INITIATOR CODON and end with a stop codon (CODON, TERMINATOR).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.Computational Biology: 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.DNA: 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).Software: Sequential operating programs and data which instruct the functioning of a digital computer.Comparative Genomic Hybridization: A method for comparing two sets of chromosomal DNA by analyzing differences in the copy number and location of specific sequences. It is used to look for large sequence changes such as deletions, duplications, amplifications, or translocations.Chromosomes, Artificial, Bacterial: DNA constructs that are composed of, at least, a REPLICATION ORIGIN, for successful replication, propagation to and maintenance as an extra chromosome in bacteria. In addition, they can carry large amounts (about 200 kilobases) of other sequence for a variety of bioengineering purposes.Genomic Instability: An increased tendency of the GENOME to acquire MUTATIONS when various processes involved in maintaining and replicating the genome are dysfunctional.DNA, Complementary: Single-stranded complementary DNA synthesized from an RNA template by the action of RNA-dependent DNA polymerase. cDNA (i.e., complementary DNA, not circular DNA, not C-DNA) is used in a variety of molecular cloning experiments as well as serving as a specific hybridization probe.Expressed Sequence Tags: Partial cDNA (DNA, COMPLEMENTARY) sequences that are unique to the cDNAs from which they were derived.Genetic Variation: Genotypic differences observed among individuals in a population.Multigene Family: 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)Sequence Homology, Amino Acid: The degree of similarity between sequences of amino acids. This information is useful for the analyzing genetic relatedness of proteins and species.Transcription, Genetic: The biosynthesis of RNA carried out on a template of DNA. The biosynthesis of DNA from an RNA template is called REVERSE TRANSCRIPTION.Models, Genetic: Theoretical representations that simulate the behavior or activity of genetic processes or phenomena. They include the use of mathematical equations, computers, and other electronic equipment.Conserved Sequence: A sequence of amino acids in a polypeptide or of nucleotides in DNA or RNA that is similar across multiple species. A known set of conserved sequences is represented by a CONSENSUS SEQUENCE. AMINO ACID MOTIFS are often composed of conserved sequences.Genome, Plant: The genetic complement of a plant (PLANTS) as represented in its DNA.DNA Primers: Short sequences (generally about 10 base pairs) of DNA that are complementary to sequences of messenger RNA and allow reverse transcriptases to start copying the adjacent sequences of mRNA. Primers are used extensively in genetic and molecular biology techniques.Promoter Regions, Genetic: DNA sequences which are recognized (directly or indirectly) and bound by a DNA-dependent RNA polymerase during the initiation of transcription. Highly conserved sequences within the promoter include the Pribnow box in bacteria and the TATA BOX in eukaryotes.Databases, Genetic: Databases devoted to knowledge about specific genes and gene products.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).Algorithms: A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.Species Specificity: 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.Blotting, Southern: A method (first developed by E.M. Southern) for detection of DNA that has been electrophoretically separated and immobilized by blotting on nitrocellulose or other type of paper or nylon membrane followed by hybridization with labeled NUCLEIC ACID PROBES.Restriction Mapping: Use of restriction endonucleases to analyze and generate a physical map of genomes, genes, or other segments of DNA.Genes: A category of nucleic acid sequences that function as units of heredity and which code for the basic instructions for the development, reproduction, and maintenance of organisms.RNA, Messenger: 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.Recombination, Genetic: Production of new arrangements of DNA by various mechanisms such as assortment and segregation, CROSSING OVER; GENE CONVERSION; GENETIC TRANSFORMATION; GENETIC CONJUGATION; GENETIC TRANSDUCTION; or mixed infection of viruses.Contig Mapping: Overlapping of cloned or sequenced DNA to construct a continuous region of a gene, chromosome or genome.Physical Chromosome Mapping: Mapping of the linear order of genes on a chromosome with units indicating their distances by using methods other than genetic recombination. These methods include nucleotide sequencing, overlapping deletions in polytene chromosomes, and electron micrography of heteroduplex DNA. (From King & Stansfield, A Dictionary of Genetics, 5th ed)Genomic Islands: Distinct units in some bacterial, bacteriophage or plasmid GENOMES that are types of MOBILE GENETIC ELEMENTS. Encoded in them are a variety of fitness conferring genes, such as VIRULENCE FACTORS (in "pathogenicity islands or islets"), ANTIBIOTIC RESISTANCE genes, or genes required for SYMBIOSIS (in "symbiosis islands or islets"). They range in size from 10 - 500 kilobases, and their GC CONTENT and CODON usage differ from the rest of the genome. They typically contain an INTEGRASE gene, although in some cases this gene has been deleted resulting in "anchored genomic islands".Phenotype: The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.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)Synteny: The presence of two or more genetic loci on the same chromosome. Extensions of this original definition refer to the similarity in content and organization between chromosomes, of different species for example.Pseudogenes: Genes bearing close resemblance to known genes at different loci, but rendered non-functional by additions or deletions in structure that prevent normal transcription or translation. When lacking introns and containing a poly-A segment near the downstream end (as a result of reverse copying from processed nuclear RNA into double-stranded DNA), they are called processed genes.Base Composition: The relative amounts of the PURINES and PYRIMIDINES in a nucleic acid.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.Sequence Homology: The degree of similarity between sequences. Studies of AMINO ACID SEQUENCE HOMOLOGY and NUCLEIC ACID SEQUENCE HOMOLOGY provide useful information about the genetic relatedness of genes, gene products, and species.Gene Duplication: Processes occurring in various organisms by which new genes are copied. Gene duplication may result in a MULTIGENE FAMILY; supergenes or PSEUDOGENES.DNA, Bacterial: Deoxyribonucleic acid that makes up the genetic material of bacteria.Plasmids: Extrachromosomal, usually CIRCULAR DNA molecules that are self-replicating and transferable from one organism to another. They are found in a variety of bacterial, archaeal, fungal, algal, and plant species. They are used in GENETIC ENGINEERING as CLONING VECTORS.Databases, Nucleic Acid: Databases containing information about NUCLEIC ACIDS such as BASE SEQUENCE; SNPS; NUCLEIC ACID CONFORMATION; and other properties. Information about the DNA fragments kept in a GENE LIBRARY or GENOMIC LIBRARY is often maintained in DNA databases.In Situ Hybridization, Fluorescence: A type of IN SITU HYBRIDIZATION in which target sequences are stained with fluorescent dye so their location and size can be determined using fluorescence microscopy. This staining is sufficiently distinct that the hybridization signal can be seen both in metaphase spreads and in interphase nuclei.Cell Line: Established cell cultures that have the potential to propagate indefinitely.Genotype: The genetic constitution of the individual, comprising the ALLELES present at each GENETIC LOCUS.Gene Library: A large collection of DNA fragments cloned (CLONING, MOLECULAR) from a given organism, tissue, organ, or cell type. It may contain complete genomic sequences (GENOMIC LIBRARY) or complementary DNA sequences, the latter being formed from messenger RNA and lacking intron sequences.Gene Order: The sequential location of genes on a chromosome.Genes, Bacterial: The functional hereditary units of BACTERIA.Oligonucleotide Array Sequence Analysis: Hybridization of a nucleic acid sample to a very large set of OLIGONUCLEOTIDE PROBES, which have been attached individually in columns and rows to a solid support, to determine a BASE SEQUENCE, or to detect variations in a gene sequence, GENE EXPRESSION, or for GENE MAPPING.Gene Expression Profiling: The determination of the pattern of genes expressed at the level of GENETIC TRANSCRIPTION, under specific circumstances or in a specific cell.RNA, Viral: Ribonucleic acid that makes up the genetic material of viruses.Gene Dosage: The number of copies of a given gene present in the cell of an organism. An increase in gene dosage (by GENE DUPLICATION for example) can result in higher levels of gene product formation. GENE DOSAGE COMPENSATION mechanisms result in adjustments to the level GENE EXPRESSION when there are changes or differences in gene dosage.Alternative Splicing: A process whereby multiple RNA transcripts are generated from a single gene. Alternative splicing involves the splicing together of other possible sets of EXONS during the processing of some, but not all, transcripts of the gene. Thus a particular exon may be connected to any one of several alternative exons to form a mature RNA. The alternative forms of mature MESSENGER RNA produce PROTEIN ISOFORMS in which one part of the isoforms is common while the other parts are different.Chromosomes, Human, Pair 22: A specific pair of GROUP G CHROMOSOMES of the human chromosome classification.Mutagenesis, Insertional: 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.Alleles: Variant forms of the same gene, occupying the same locus on homologous CHROMOSOMES, and governing the variants in production of the same gene product.Genetic Markers: A phenotypically recognizable genetic trait which can be used to identify a genetic locus, a linkage group, or a recombination event.Internet: A loose confederation of computer communication networks around the world. The networks that make up the Internet are connected through several backbone networks. The Internet grew out of the US Government ARPAnet project and was designed to facilitate information exchange.DNA Mutational Analysis: Biochemical identification of mutational changes in a nucleotide sequence.Regulatory Sequences, Nucleic Acid: Nucleic acid sequences involved in regulating the expression of genes.Escherichia coli: 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.Transcription Factors: Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process.Bacterial Proteins: Proteins found in any species of bacterium.Genome, Fungal: The complete gene complement contained in a set of chromosomes in a fungus.DNA, Viral: Deoxyribonucleic acid that makes up the genetic material of viruses.Genomic Imprinting: The variable phenotypic expression of a GENE depending on whether it is of paternal or maternal origin, which is a function of the DNA METHYLATION pattern. Imprinted regions are observed to be more methylated and less transcriptionally active. (Segen, Dictionary of Modern Medicine, 1992)Binding Sites: The parts of a macromolecule that directly participate in its specific combination with another molecule.Polymorphism, Single Nucleotide: A single nucleotide variation in a genetic sequence that occurs at appreciable frequency in the population.Gene Expression Regulation: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control (induction or repression) of gene action at the level of transcription or translation.Polymorphism, Genetic: The regular and simultaneous occurrence in a single interbreeding population of two or more discontinuous genotypes. The concept includes differences in genotypes ranging in size from a single nucleotide site (POLYMORPHISM, SINGLE NUCLEOTIDE) to large nucleotide sequences visible at a chromosomal level.DNA, Plant: Deoxyribonucleic acid that makes up the genetic material of plants.Genes, Plant: The functional hereditary units of PLANTS.DNA-Binding Proteins: Proteins which bind to DNA. The family includes proteins which bind to both double- and single-stranded DNA and also includes specific DNA binding proteins in serum which can be used as markers for malignant diseases.Sequence Tagged Sites: Short tracts of DNA sequence that are used as landmarks in GENOME mapping. In most instances, 200 to 500 base pairs of sequence define a Sequence Tagged Site (STS) that is operationally unique in the human genome (i.e., can be specifically detected by the polymerase chain reaction in the presence of all other genomic sequences). The overwhelming advantage of STSs over mapping landmarks defined in other ways is that the means of testing for the presence of a particular STS can be completely described as information in a database.Molecular Sequence Annotation: The addition of descriptive information about the function or structure of a molecular sequence to its MOLECULAR SEQUENCE DATA record.Gene Components: The parts of the gene sequence that carry out the different functions of the GENES.RNA Splicing: The ultimate exclusion of nonsense sequences or intervening sequences (introns) before the final RNA transcript is sent to the cytoplasm.Saccharomyces cerevisiae: A species of the genus SACCHAROMYCES, family Saccharomycetaceae, order Saccharomycetales, known as "baker's" or "brewer's" yeast. The dried form is used as a dietary supplement.Gene Rearrangement: The ordered rearrangement of gene regions by DNA recombination such as that which occurs normally during development.Viral Proteins: Proteins found in any species of virus.Oryza sativa: Annual cereal grass of the family POACEAE and its edible starchy grain, rice, which is the staple food of roughly one-half of the world's population.Gene Expression: The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION.Cluster Analysis: A set of statistical methods used to group variables or observations into strongly inter-related subgroups. In epidemiology, it may be used to analyze a closely grouped series of events or cases of disease or other health-related phenomenon with well-defined distribution patterns in relation to time or place or both.Takifugu: A genus of pufferfish commonly used for research.Software Validation: The act of testing the software for compliance with a standard.Pan troglodytes: The common chimpanzee, a species of the genus Pan, family HOMINIDAE. It lives in Africa, primarily in the tropical rainforests. There are a number of recognized subspecies.Genes, Viral: The functional hereditary units of VIRUSES.Reverse Transcriptase Polymerase Chain Reaction: A variation of the PCR technique in which cDNA is made from RNA via reverse transcription. The resultant cDNA is then amplified using standard PCR protocols.Sequence Analysis: A multistage process that includes the determination of a sequence (protein, carbohydrate, etc.), its fragmentation and analysis, and the interpretation of the resulting sequence information.Chromosome Aberrations: Abnormal number or structure of chromosomes. Chromosome aberrations may result in CHROMOSOME DISORDERS.Human Genome Project: A coordinated effort of researchers to map (CHROMOSOME MAPPING) and sequence (SEQUENCE ANALYSIS, DNA) the human GENOME.Nucleic Acid Conformation: The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.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.User-Computer Interface: The portion of an interactive computer program that issues messages to and receives commands from a user.Sequence Analysis, RNA: A multistage process that includes cloning, physical mapping, subcloning, sequencing, and information analysis of an RNA SEQUENCE.Mutagenesis: Process of generating a genetic MUTATION. It may occur spontaneously or be induced by MUTAGENS.Microsatellite Repeats: A variety of simple repeat sequences that are distributed throughout the GENOME. They are characterized by a short repeat unit of 2-8 basepairs that is repeated up to 100 times. They are also known as short tandem repeats (STRs).INDEL Mutation: A mutation named with the blend of insertion and deletion. It refers to a length difference between two ALLELES where it is unknowable if the difference was originally caused by a SEQUENCE INSERTION or by a SEQUENCE DELETION. If the number of nucleotides in the insertion/deletion is not divisible by three, and it occurs in a protein coding region, it is also a FRAMESHIFT MUTATION.Chromosomes, Artificial, P1 Bacteriophage: DNA constructs that are derived from the DNA of BACTERIOPHAGE P1. They can carry large amounts (about 100-300 kilobases) of other sequence for a variety of bioengineering purposes.Genetic Complementation Test: A test used to determine whether or not complementation (compensation in the form of dominance) will occur in a cell with a given mutant phenotype when another mutant genome, encoding the same mutant phenotype, is introduced into that cell.Point Mutation: A mutation caused by the substitution of one nucleotide for another. This results in the DNA molecule having a change in a single base pair.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.Virulence: The degree of pathogenicity within a group or species of microorganisms or viruses as indicated by case fatality rates and/or the ability of the organism to invade the tissues of the host. The pathogenic capacity of an organism is determined by its VIRULENCE FACTORS.Gene Amplification: A selective increase in the number of copies of a gene coding for a specific protein without a proportional increase in other genes. It occurs naturally via the excision of a copy of the repeating sequence from the chromosome and its extrachromosomal replication in a plasmid, or via the production of an RNA transcript of the entire repeating sequence of ribosomal RNA followed by the reverse transcription of the molecule to produce an additional copy of the original DNA sequence. Laboratory techniques have been introduced for inducing disproportional replication by unequal crossing over, uptake of DNA from lysed cells, or generation of extrachromosomal sequences from rolling circle replication.Genetic Linkage: The co-inheritance of two or more non-allelic GENES due to their being located more or less closely on the same CHROMOSOME.Genes, Fungal: The functional hereditary units of FUNGI.Genome, Protozoan: The complete genetic complement contained in a set of CHROMOSOMES in a protozoan.Drosophila melanogaster: A species of fruit fly much used in genetics because of the large size of its chromosomes.Genome, Archaeal: The genetic complement of an archaeal organism (ARCHAEA) as represented in its DNA.Chromosomes, Human, Pair 7: A specific pair of GROUP C CHROMOSOMES of the human chromosome classification.Transfection: The uptake of naked or purified DNA by CELLS, usually meaning the process as it occurs in eukaryotic cells. It is analogous to bacterial transformation (TRANSFORMATION, BACTERIAL) and both are routinely employed in GENE TRANSFER TECHNIQUES.Pedigree: The record of descent or ancestry, particularly of a particular condition or trait, indicating individual family members, their relationships, and their status with respect to the trait or condition.Genomic Structural Variation: Contiguous large-scale (1000-400,000 basepairs) differences in the genomic DNA between individuals, due to SEQUENCE DELETION; SEQUENCE INSERTION; or SEQUENCE INVERSION.Biological Evolution: The process of cumulative change over successive generations through which organisms acquire their distinguishing morphological and physiological characteristics.Retroelements: Elements that are transcribed into RNA, reverse-transcribed into DNA and then inserted into a new site in the genome. Long terminal repeats (LTRs) similar to those from retroviruses are contained in retrotransposons and retrovirus-like elements. Retroposons, such as LONG INTERSPERSED NUCLEOTIDE ELEMENTS and SHORT INTERSPERSED NUCLEOTIDE ELEMENTS do not contain LTRs.Segmental Duplications, Genomic: Low-copy (2-50) repetitive DNA elements that are highly homologous and range in size from 1000 to 400,000 base pairs.Chromosome Breakage: A type of chromosomal aberration involving DNA BREAKS. Chromosome breakage can result in CHROMOSOMAL TRANSLOCATION; CHROMOSOME INVERSION; or SEQUENCE DELETION.Homozygote: An individual in which both alleles at a given locus are identical.Databases, Factual: Extensive collections, reputedly complete, of facts and data garnered from material of a specialized subject area and made available for analysis and application. The collection can be automated by various contemporary methods for retrieval. The concept should be differentiated from DATABASES, BIBLIOGRAPHIC which is restricted to collections of bibliographic references.Blotting, Northern: Detection of RNA that has been electrophoretically separated and immobilized by blotting on nitrocellulose or other type of paper or nylon membrane followed by hybridization with labeled NUCLEIC ACID PROBES.Consensus Sequence: 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.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.DNA, Intergenic: Any of the DNA in between gene-coding DNA, including untranslated regions, 5' and 3' flanking regions, INTRONS, non-functional pseudogenes, and non-functional repetitive sequences. This DNA may or may not encode regulatory functions.Tandem Repeat Sequences: Copies of DNA sequences which lie adjacent to each other in the same orientation (direct tandem repeats) or in the opposite direction to each other (INVERTED TANDEM REPEATS).DNA, Fungal: Deoxyribonucleic acid that makes up the genetic material of fungi.Chromosomes, Artificial: DNA constructs that are composed of, at least, elements such as a REPLICATION ORIGIN; TELOMERE; and CENTROMERE, that are required for successful replication, propagation to and maintenance in progeny cells. In addition, they are constructed to carry other sequences for analysis or gene transfer.Chromosomes, Bacterial: Structures within the nucleus of bacterial cells consisting of or containing DNA, which carry genetic information essential to the cell.Alu Elements: The Alu sequence family (named for the restriction endonuclease cleavage enzyme Alu I) is the most highly repeated interspersed repeat element in humans (over a million copies). It is derived from the 7SL RNA component of the SIGNAL RECOGNITION PARTICLE and contains an RNA polymerase III promoter. Transposition of this element into coding and regulatory regions of genes is responsible for many heritable diseases.Data Compression: Information application based on a variety of coding methods to minimize the amount of data to be stored, retrieved, or transmitted. Data compression can be applied to various forms of data, such as images and signals. It is used to reduce costs and increase efficiency in the maintenance of large volumes of data.Gene Transfer, Horizontal: The naturally occurring transmission of genetic information between organisms, related or unrelated, circumventing parent-to-offspring transmission. Horizontal gene transfer may occur via a variety of naturally occurring processes such as GENETIC CONJUGATION; GENETIC TRANSDUCTION; and TRANSFECTION. It may result in a change of the recipient organism's genetic composition (TRANSFORMATION, GENETIC).Codon: 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).Plant Proteins: Proteins found in plants (flowers, herbs, shrubs, trees, etc.). The concept does not include proteins found in vegetables for which VEGETABLE PROTEINS is available.Bacteriophages: Viruses whose hosts are bacterial cells.Computer Graphics: The process of pictorial communication, between human and computers, in which the computer input and output have the form of charts, drawings, or other appropriate pictorial representation.Polymorphism, Restriction Fragment Length: Variation occurring within a species in the presence or length of DNA fragment generated by a specific endonuclease at a specific site in the genome. Such variations are generated by mutations that create or abolish recognition sites for these enzymes or change the length of the fragment.GC Rich Sequence: A nucleic acid sequence that contains an above average number of GUANINE and CYTOSINE bases.Protein Binding: The process in which substances, either endogenous or exogenous, bind to proteins, peptides, enzymes, protein precursors, or allied compounds. Specific protein-binding measures are often used as assays in diagnostic assessments.Chickens: Common name for the species Gallus gallus, the domestic fowl, in the family Phasianidae, order GALLIFORMES. It is descended from the red jungle fowl of SOUTHEAST ASIA.Chromosomes, Plant: Complex nucleoprotein structures which contain the genomic DNA and are part of the CELL NUCLEUS of PLANTS.Genetic Loci: Specific regions that are mapped within a GENOME. Genetic loci are usually identified with a shorthand notation that indicates the chromosome number and the position of a specific band along the P or Q arm of the chromosome where they are found. For example the locus 6p21 is found within band 21 of the P-arm of CHROMOSOME 6. Many well known genetic loci are also known by common names that are associated with a genetic function or HEREDITARY DISEASE.RNA: 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)Organ Specificity: Characteristic restricted to a particular organ of the body, such as a cell type, metabolic response or expression of a particular protein or antigen.Arabidopsis: A plant genus of the family BRASSICACEAE that contains ARABIDOPSIS PROTEINS and MADS DOMAIN PROTEINS. The species A. thaliana is used for experiments in classical plant genetics as well as molecular genetic studies in plant physiology, biochemistry, and development.Gene Expression Regulation, Bacterial: Any of the processes by which cytoplasmic or intercellular factors influence the differential control of gene action in bacteria.Genes, Insect: The functional hereditary units of INSECTS.Cosmids: Plasmids containing at least one cos (cohesive-end site) of PHAGE LAMBDA. They are used as cloning vehicles.Untranslated Regions: The parts of the messenger RNA sequence that do not code for product, i.e. the 5' UNTRANSLATED REGIONS and 3' UNTRANSLATED REGIONS.Terminal Repeat Sequences: Nucleotide sequences repeated on both the 5' and 3' ends of a sequence under consideration. For example, the hallmarks of a transposon are that it is flanked by inverted repeats on each end and the inverted repeats are flanked by direct repeats. The Delta element of Ty retrotransposons and LTRs (long terminal repeats) are examples of this concept.Fungal Proteins: Proteins found in any species of fungus.Frameshift Mutation: A type of mutation in which a number of NUCLEOTIDES deleted from or inserted into a protein coding sequence is not divisible by three, thereby causing an alteration in the READING FRAMES of the entire coding sequence downstream of the mutation. These mutations may be induced by certain types of MUTAGENS or may occur spontaneously.5' Untranslated Regions: The sequence at the 5' end of the messenger RNA that does not code for product. This sequence contains the ribosome binding site and other transcription and translation regulating sequences.Genome, Insect: The genetic complement of an insect (INSECTS) as represented in its DNA.Oligonucleotide Probes: 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.Mice, Inbred C57BLRecombinant Fusion Proteins: Recombinant proteins produced by the GENETIC TRANSLATION of fused genes formed by the combination of NUCLEIC ACID REGULATORY SEQUENCES of one or more genes with the protein coding sequences of one or more genes.Carrier Proteins: Transport proteins that carry specific substances in the blood or across cell membranes.Mice, Knockout: Strains of mice in which certain GENES of their GENOMES have been disrupted, or "knocked-out". To produce knockouts, using RECOMBINANT DNA technology, the normal DNA sequence of the gene being studied is altered to prevent synthesis of a normal gene product. Cloned cells in which this DNA alteration is successful are then injected into mouse EMBRYOS to produce chimeric mice. The chimeric mice are then bred to yield a strain in which all the cells of the mouse contain the disrupted gene. Knockout mice are used as EXPERIMENTAL ANIMAL MODELS for diseases (DISEASE MODELS, ANIMAL) and to clarify the functions of the genes.Enhancer Elements, Genetic: Cis-acting DNA sequences which can increase transcription of genes. Enhancers can usually function in either orientation and at various distances from a promoter.Membrane Proteins: Proteins which are found in membranes including cellular and intracellular membranes. They consist of two types, peripheral and integral proteins. They include most membrane-associated enzymes, antigenic proteins, transport proteins, and drug, hormone, and lectin receptors.Recombinant Proteins: Proteins prepared by recombinant DNA technology.High-Throughput Nucleotide Sequencing: Techniques of nucleotide sequence analysis that increase the range, complexity, sensitivity, and accuracy of results by greatly increasing the scale of operations and thus the number of nucleotides, and the number of copies of each nucleotide sequenced. The sequencing may be done by analysis of the synthesis or ligation products, hybridization to preexisting sequences, etc.Heterozygote: An individual having different alleles at one or more loci regarding a specific character.Chordopoxvirinae: A subfamily of the family POXVIRIDAE, containing eight genera comprising all the vertebrate poxviruses.RNA Splice Sites: Nucleotide sequences located at the ends of EXONS and recognized in pre-messenger RNA by SPLICEOSOMES. They are joined during the RNA SPLICING reaction, forming the junctions between exons.Nuclear Proteins: Proteins found in the nucleus of a cell. Do not confuse with NUCLEOPROTEINS which are proteins conjugated with nucleic acids, that are not necessarily present in the nucleus.DNA Copy Number Variations: Stretches of genomic DNA that exist in different multiples between individuals. Many copy number variations have been associated with susceptibility or resistance to disease.Selection, Genetic: Differential and non-random reproduction of different genotypes, operating to alter the gene frequencies within a population.Saccharomyces cerevisiae Proteins: Proteins obtained from the species SACCHAROMYCES CEREVISIAE. The function of specific proteins from this organism are the subject of intense scientific interest and have been used to derive basic understanding of the functioning similar proteins in higher eukaryotes.Gene Expression Regulation, Developmental: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action during the developmental stages of an organism.Haplotypes: The genetic constitution of individuals with respect to one member of a pair of allelic genes, or sets of genes that are closely linked and tend to be inherited together such as those of the MAJOR HISTOCOMPATIBILITY COMPLEX.Genetic Techniques: Chromosomal, biochemical, intracellular, and other methods used in the study of genetics.Ursidae: The family of carnivorous or omnivorous bears, having massive bodies, coarse heavy fur, relatively short limbs, and almost rudimentary tails.DNA, Neoplasm: DNA present in neoplastic tissue.Prophages: Genomes of temperate BACTERIOPHAGES integrated into the DNA of their bacterial host cell. The prophages can be duplicated for many cell generations until some stimulus induces its activation and virulence.Clonal Deletion: Removal, via CELL DEATH, of immature lymphocytes that interact with antigens during maturation. For T-lymphocytes this occurs in the thymus and ensures that mature T-lymphocytes are self tolerant. B-lymphocytes may also undergo clonal deletion.DNA Methylation: Addition of methyl groups to DNA. DNA methyltransferases (DNA methylases) perform this reaction using S-ADENOSYLMETHIONINE as the methyl group donor.Genes, Overlapping: Genes whose nucleotide sequences overlap to some degree. The overlapped sequences may involve structural or regulatory genes of eukaryotic or prokaryotic cells.Genome Size: The amount of DNA (or RNA) in one copy of a genome.Quantitative Trait Loci: Genetic loci associated with a QUANTITATIVE TRAIT.
Large-scale mutations involve the deletion or gain of a portion of a chromosome. Genomic amplification occurs when a cell gains ... More common are mutations, which are changes in the nucleotide sequence of genomic DNA. ... In addition, frequent epigenetic alterations of the DNA sequences code for small RNAs called microRNAs (or miRNAs). miRNAs do ... Disruption of a single gene may also result from integration of genomic material from a DNA virus or retrovirus, leading to the ...
Many of these changes are mutations, or changes in the nucleotide sequence of genomic DNA. There are also many epigenetic ... Large-scale mutations involve the deletion or gain of a portion of a chromosome. Genomic amplification occurs when a cell gains ... February 2001). "Initial sequencing and analysis of the human genome". Nature. 409 (6822): 860-921. Bibcode:2001Natur.409..860L ... Disruption of a single gene may also result from integration of genomic material from a DNA virus or retrovirus, and such an ...
... which are changes in the nucleotide sequence of genomic DNA. Large-scale mutations involve the deletion or gain of a portion of ... In addition, frequent epigenetic alterations of the DNA sequences code for small RNAs called microRNAs (or miRNAs). miRNAs do ... Genomic amplification occurs when a cell gains copies (often 20 or more) of a small chromosomal locus, usually containing one ... Disruption of a single gene may also result from integration of genomic material from a DNA virus or retrovirus, leading to the ...
... re-analysis of the original genomic data often leads to modifications of the genomic sequence. The changes in the genomic ... The protein products of gene are created by translating the CDS sequences. Each unique protein sequence is given a unique ... Many of these changes were single nucleotide insertions or deletions, however several large mis-assemblies have been uncovered ... Sequence curation at WormBase refers to the maintenance and annotation of the primary genomic sequence and a consensus gene set ...
Complete nucleic acid sequence and genomic organization". FEBS Lett. 213 (1): 221-6. doi:10.1016/0014-5793(87)81495-3. PMID ... Electron microscopic analysis of RNA:DNA hybrids, complete nucleotide sequence, and identification of 5' homologous sequences ... 1989). "A deletion mutation in the ApoC-II gene (ApoC-II Nijmegen) of a patient with a deficiency of apolipoprotein C-II". J. ... cDNA sequences and mRNA abundance". Nucleic Acids Res. 12 (9): 3917-32. doi:10.1093/nar/12.9.3917. PMC 318799. PMID 6328445.. ...
... gene deletions, and short sequence insertions in several genomic loci with increased efficiency and time sensitivity. The λ-red ... In this system, sequences matching foreign bacteriophage or plasmid DNA are incorporated as "spacer" sequences into the ... Of this sequence, at least 15 base pairs should be homologous to the target sequence at both the 5' and 3' ends to provide ... The SCAR-less method is able to induce point mutations, oligonucleotide-mediated deletions, and short sequence insertions with ...
In mammalian cells, the presence of such sequences was found to produce large genomic fragment deletions due to chromosomal ... The greatest increase in activity is observed when the Z-DNA sequence is placed three helical turns after the promoter sequence ... A study on Escherichia coli found that gene deletions spontaneously occur in plasmid regions containing Z-DNA-forming sequences ... 1989). "Z-DNA-forming sequences are spontaneous deletion hot spots". Proceedings of the National Academy of Sciences of the ...
Whole genome sequencing of C. elegans modified with a pair of 5-finger ZFNs found only the intended modification and a deletion ... Multiple pairs of ZFNs can also be used to completely remove entire large segments of genomic sequence. To monitor the editing ... It is also hoped that, when applied to non-HIV infected persons, this strategy could offer a genomic vaccine against HIV and ... Each set of zinc fingers is specific to a nucleotide sequence on either side of the targeted gene 5-7 bp separation between ...
The curated VBRC database contains all publicly available genomic sequences for seven of the virus families covered under the ... a program designed to align a nucleotide and protein sequence, taking terminal gaps and insertion/deletion mutations into ... This level contains information about the virus species or isolate and its entire genomic sequence. Annotated genes. This level ... GFS (Genome Fingerprint Scanning) maps peptide mass fingerprint data to genomic sequences. It is built into VOCS. NAP ( ...
... alters the amino acid sequence of the encoded protein so that it differs from that predicted by the genomic DNA sequence. RNA ... which contains complementary sequences to the regions around the insertion/deletion points. The newly formed double-stranded ... those formed in an mRNA where intronic sequence base pairs with a complementary exonic sequence), while promiscuous editing ... In the intestines, the mRNA has a CAA sequence edited to be UAA, a stop codon, thus producing the shorter B48 form. C-to-U ...
"Comparative sequencing of human and chimpanzee MHC class I regions unveils insertions/deletions as the major path to genomic ... nucleotide sequence identity) drops to only 86.7%. For example, a large deletion of 95 kilobases (kb) between the loci of the ... BGI Shenzhen and the National Human Genome Research Institute's Large-Scale Sequencing Network are planning to sequence a ... are going to be sequenced with deep coverage (20x per genome). The third pilot study involves sequencing the coding regions ( ...
... was a high-level programming environment for examining genomic sequences. It supported the matching of genomic sequences in ... The use of multiple sequence information to predict secondary structure of proteins became popular as a result of the work of ... and deletions. Building on Darwin, the Benner laboratory provided tools to predict the three dimensional structure of proteins ... In the late 1980s, Benner recognized the potential for genome sequencing projects to generate millions of sequences and enable ...
DNA sequencing is used to directly analyze the genomic DNA sequence of a particular gene. In general, only the parts of the ... Examples of chromosome abnormalities include aneuploidy, chromosomal rearrangements, and genomic deletion/duplication disorders ... genomic deletions or duplications, characterizing chromosomal translocations and determining the origin of ring chromosomes. ... Array comparative genomic hybridization is a new molecular technique that involves hybridization of an individual DNA sample to ...
This is exemplified in E. coli, where genomic sequences with long inverted repeats are seldom replicated, but rather deleted ... the composite sequence is a palindromic sequence. For example, 5'---TTACGnnnnnnCGTAA---3' is an inverted repeat sequence. Both ... resulting in an equally very high rate of deletion. Finally, a very high rate of deletion and recombination were also observed ... The limited recombination of the sequences between two distinct sequence elements known as conservative site-specific ...
For genomic re-sequencing and newly sequenced genomes, a de-novo assembly will be provided. 2. The Genomatix Genome Analyzer ( ... which allows for input of raw sequence reads plus optional quality files from any deep sequencing hardware. It provides ultra ... with no practical limits on the number of point mutations and/or insertions and deletions that can be taken into account during ... Analysis technology for high throughput genomic technologies (microarrays and next generation sequencing) Literature mining ...
... was initially sequenced as part of the Full-length long Japan genomic sequencing project. FAM46C is found on chromosome ... Deletion and/ or mutation of FAM46C has been associated with impaired overall survival in Myeloma patients. Homo sapiens FAM46C ... Based on multiple sequence alignments generated by ClustalW an unrooted phylogenetic tree was generated for select FAM46C ... 1] - The homepage of the Full-length long Japan human genomic sequencing project. ...
... account for a large proportion of the genomic sequences in many species. Alu sequences, classified as a short interspersed ... because the insulator indicates where an enhanced or repressed sequence ends. Shared sequences of apparently non-functional DNA ... for example deletion or insertion, does not have a frameshift effect on the whole chromosome. When genome complexity is ... Pseudogene sequences appear to accumulate mutations more rapidly than coding sequences due to a loss of selective pressure. ...
"Structure of human osteonectin based upon analysis of cDNA and genomic sequences". Biochemistry. 28 (15): 6483-91. doi:10.1021/ ... Male and female animals underwent a standardized phenotypic screen to determine the effects of deletion. Twenty six tests were ... Swaroop A, Hogan BL, Francke U (Jan 1988). "Molecular analysis of the cDNA for human SPARC/osteonectin/BM-40: sequence, ... Lankat-Buttgereit B, Mann K, Deutzmann R, Timpl R, Krieg T (Aug 1988). "Cloning and complete amino acid sequences of human and ...
... tracks chromosome deletions and or amplifications using fluorescent dyes on genomic sequences of DNA samples. The DNA samples ( ... In turn, this allows scientists to map out a person's DNA sequence allowing for a diagnosis to be made. Due to its recent ... The greater the deletions, the greater the severity of the condition. However, in recent studies, 9q34 deletion syndrome occurs ... 9q34 deletion syndrome, also known as Kleefstra syndrome, is a rare genetic disorder. Terminal deletions of chromosome 9q34 ...
To detect the specific breakpoints at which a deletion occurs, or to detect genomic lesions introduced by a duplication or ... From a computational perspective, microfluidic Sanger sequencing is still the most effective way to sequence and assemble ... When sequencing a genome, it must be broken down into pieces that are short enough to be sequenced in a single read. These ... Sequencing technologies that generate long reads, including transmission electron microscopy DNA sequencing, can capture entire ...
Comparative analysis of genomic sequences have also identified five conserved signature indels in important proteins which are ... 1998). "The genome sequence of Rickettsia prowazekii and the origin of mitochondria". Nature. 396 (6707): 133-40. doi:10.1038/ ... and a one-amino-acid deletion in exonuclease VII. These indels are all characteristic of the genus and serve as molecular ... The cladogram of Rickettsidae has been inferred by Ferla et al. [13] from the comparison of 16S + 23S ribosomal RNA sequences. ...
Interestingly, when the genomic sequence (1530600 - 1531700) of the protein from Arthrobacter is obtained, it is found that it ... Strand slippage deletion (illegitimate recombination) may be responsible. The presence of two palindromes in the regional ... Hence TMEM20, TMEM22, AMAC1 and AMAC-like (AMAC1L1, AMAC1L2, AMAC1L3) sequences have been renamed to SLC35Gs in RefSeq for ... If a sequence contains an inverted repeat (a palindrome) longer than 10 bp, and a spacer/insert of less than 75-150 basepairs, ...
meaning that an exogenous DNA sequence can be targeted to a specific genomic position (a technique called gene targeting) to ... The targeted deletion or alteration of moss genes relies on the integration of a short DNA strand at a defined position in the ... The genome of P. patens, with about 500 megabase pairs organized into 27 chromosomes, was completely sequenced in 2006. ... The genome sequence of P. patens has revealed the presence of numerous genes that encode proteins necessary for repair of DNA ...
1988). "Human esterase D gene: complete cDNA sequence, genomic structure, and application in the genetic diagnosis of human ... 2004). "Complete sequencing and characterization of 21,243 full-length human cDNAs". Nat. Genet. 36 (1): 40-5. doi:10.1038/ ... 1991). "[Lausanne study of retinoblastoma, 1986-90: deletion of esterase D locus in a collective of 128 patients]". Klinische ... 2004). "The DNA sequence and analysis of human chromosome 13". Nature. 428 (6982): 522-8. doi:10.1038/nature02379. PMC 2665288 ...
Choosing a consensus reference sequence over a more specific reference sequence (e.g., the revised Cambridge Reference Sequence ... single nucleotide substitutions and insertions/deletions) need to be recorded, thereby greatly reducing the amount of ... this is typically the case in genomic sequence data). The compression ratio of currently available genomic data compression ... microsatellite sequences) or many sequences exhibit high levels of similarity (e.g., multiple genome sequences from the same ...
... both very common in chloroplast transit sequences-making up 20-30% of the sequence)[45] are often the amino acids that accept ... RNA editing is the insertion, deletion, and substitution of nucleotides in a mRNA transcript prior to translation to protein. ... "Genomic footprints of a cryptic plastid endosymbiosis in diatoms" (PDF). Science. 324 (5935): 1724-6. Bibcode:2009Sci... ... Its existence was first proven in 1962,[4] and first sequenced in 1986-when two Japanese research teams sequenced the ...
Genomic Sequencing of a BAC-Based Clone of HCMV Towne Strain. A construct, TowneBAC, was produced by inserting a BAC sequence ... The deletion cassette was designed to remove the entire coding sequence for a given ORF. Although ≈10% of HCMV ORFs overlapped ... Genomic Sequencing and Bioinformatic Analysis. TowneBAC DNAs were subjected to genomewide shotgun sequencing analysis at MWG ... Similar to the sequence of HCMV AD169 strain, which is the only other complete HCMV genome that has been sequenced (10), the ...
Six multi-exon deletions and four single-exon deletions were detected. Using MLPA in addition to sequencing, we expanded the ... This study wanted to assess the importance of deletions and insertions in the ABCC6 genomic region, which is known to have a ... To detect ABCC6 deletions/insertions, which can be missed by direct sequencing, multiplex ligation-dependent probe ... Our results further illustrate the instability of the ABCC6 genomic region and stress the importance of screening for deletions ...
NISC Comparative Sequencing Program. Distribution and intensity of constraint in mammalian genomic sequence. Genome Res. 2005; ... Identification and Analysis of Insertion/Deletion Polymorphisms. Insertions/deletions (Indels) were annotated using the Variant ... Sequencing depth is also a major consideration for sequencing studies. Next generation sequencing technologies have a higher ... 6 Options include whole exome sequencing (WES) and whole genome sequencing (WGS). WES interrogates only the coding sequence and ...
Large-scale mutations involve the deletion or gain of a portion of a chromosome. Genomic amplification occurs when a cell gains ... More common are mutations, which are changes in the nucleotide sequence of genomic DNA. ... In addition, frequent epigenetic alterations of the DNA sequences code for small RNAs called microRNAs (or miRNAs). miRNAs do ... Disruption of a single gene may also result from integration of genomic material from a DNA virus or retrovirus, leading to the ...
deletion; +, insertion. Red characters represent nucleotides that do not match the genomic sequence. The blue sequences are the ... Sequence analysis of the PCR products derived from this animal showed both a small deletion and the wild-type sequence, ... Sequence analysis of PCR products derived from the mutant F1 animals showed small deletions at one site or deletions that ... Target sequences of the sgRNAs are underlined within the genomic sequences of the corresponding genes. The nature of the ...
The sequence of the published cDNA (2) and a genomic DNA sequence obtained from GenBank (accession AL138899) were used as the ... The sense sequences for the two oligonucleotides with the deletion of the respective putative SP1 element were 5′-GAG TGC GCA ... The sequence AGCGG was also present in the oligo that had the deletion of SP1 element (−40 to −45) shown in lane 4. ... Analysis of the genomic DNA sequence covering the dual CD1D promoters. The region covering the proximal and the distal promoter ...
We have previously investigated the pattern of genetic differentiation among human populations at 36.8 million genomic variants ... We considered 36.8 million genomic variants (35,587,323 SNPs; 1,244,127 small insertion/deletions (INDELs); 13,110 large ... Chen GK, Marjoram P, Wall JD: Fast and flexible simulation of DNA sequence data. Genome Res. 2009, 19: 136-142.PubMedPubMed ... Human genomic regions with exceptionally high levels of population differentiation identified from 911 whole-genome sequences. ...
This massively parallel sequence analysis (MitomeNGS) will not detect genomic structural rearrangements (eg. deletions, ... Mutations and novel variants are confirmed by Sanger sequencing.. Sequence Analysis for the 10 genes in the Mitochondrial ... Targeted Capture followed by Massively Parallel Sequencing. Gene Name:. COX10, COX15, COX4I2, COX6B1, FASTKD2, LRPPRC, SCO1, ... All exons of these 10 genes are examined by NGS and Sanger Sequencing. Exonic variants and intronic variants within 20bp of the ...
Recent whole-genome sequencing studies of neuroblatoma did not find genomic aberrations of the BAP1 locus44. However, 3p ... Deletion of chromosome 3p was also non-randomly associated with deletion of chromosome 11q in neuroblastoma41. Furthermore, ... The Orbitrap mass spectra of the quadruply charged 1433S peptide sequence 191-224 (m/z 836.9045) enabled mass determination of ... Coordinate deletion of chromosome 3p and 11q in neuroblastoma detected by comparative genomic hybridization. Cancer Genet. ...
Mutant strains were confirmed by sequencing of genomic DNA.. The ADA2, SPT7, SPT8, MDH1, and PHO84 deletion strains were all ... The SPT7 sequence was verified by DNA sequencing. Site-directed mutagenesis was performed to create the L1141V, L1142V, and ... Deletion of this gene does not curtail the RLS of the cells (Kirchman et al. 1999). Deletion of MDH1 and BAP2, individually, ... The effect of SPT7 deletion (Figure 2B) or GCN5 deletion (Kim et al. 2004) on RLS in rho0 cells was very similar. RLS was ...
... raw sequenced data was transferred to the LifeScope Genomic Analysis server for secondary analysis. Sequence reads were mapped ... The third family presented heterozygous deletions p.delF1617 in S3-S4 linker of domain IV and the missense p.R1632H in S4 ... With the advantages of next-generation sequencing especially whole exome sequencing that can explore the sequence of all exons ... Moreover, by direct sequencing and whole exome sequencing, variants in the CACNA1C gene, which are the common causes of both ...
VAV1 intron 25-exon 26 deletion-induced missplicing and VAV1 Δ778-786 expression. (A) Genomic DNA sequences for PTCLs with ... P scores indicate the Z value for sequence over/underrepresentation in internal noncoding exons vs. pseudo exons. I scores ... B) Genomic DNA and cDNA sequences corresponding to the intron 25-exon 26 genomic DNA and exon 25-exon 26 cDNA boundaries, ... Using RNA sequencing and targeted sequencing, here we identify a recurrent in-frame deletion (VAV1 Δ778-786) generated by a ...
Twenty clones lost their WT allele and contained the genomic deletion. Sequencing confirmed the proper deletion of CASP in ... Sequence alignment.. Protein sequence alignments were performed by Vector NTI software 9.0.0 using the BLOSUM62 mt2 matrix. ... Deletion of exons 15-17 of CASP eliminated CASP expression (Fig. 4C,D). Also, deletion of CASP did not affect the distribution ... 4B) and sequencing of amplicons (data not shown) confirmed accurate deletion of CASP exons 15-17 in selected SV40-transformed ...
A mutation is essentially a genetic typo -- an addition, deletion or alteration in the genomic sequence. Mutations in the ... Protein-coding sequences make up less than two percent of your whole genome. All of these genes are present in cells throughout ... as a program that can read a raw sequence of DNA and predict the corresponding effect on gene expression. ...
Linked read sequencing retains long-range genomic information by enabling sequence reads to be derived from HMW DNA molecules, ... We illustrate how the different component SVs such as the genomic deletions and inversion led to a common genomic motif that ... After sequencing, the barcoded sequence reads provide long range genomic information, identify individual high molecular weight ... The genomic deletion of Cdh1 and Trp53 was confirmed by PCR.. To model the effect of the FGFR2 amplification event in the two ...
... and near-target sequence. "Mean target coverage" represents the average number of unique reads in which each base was sequenced ... Abbreviations: amp, amplification; del, deletion.. *. ↵a Clinically validated and approved alterations (for tier 1 or ... NOTE: Barcoded and pooled genomic DNA from FFPE tumor samples was subjected to exon capture and sequenced in a single 100-bp ... D, sequence coverage for each target exon in breast cancer cell line MDA-MB-231 compared with a normal diploid sample. Targets ...
Nearly 400-fold mean sequence coverage was achieved, and single-nucleotide sequence variants, small insertions/deletions, and ... We sequenced 100 bases from both ends of library DNA fragments by using an Illumina HiSeq 2000 instrument. The sequence reads ... and genomic alterations (single-nucleotide sequence variants, small insertions/deletions, and DNA copy-number alterations) were ... We describe a sequencing-based approach to identifying genomic alterations in FFPE tumor samples. These studies affirm the ...
Genomic sequencing and PCR analysis identified the mutation as a 51.5 kb deletion. The deleted region contains all Gli3 coding ... expressed sequence AU023367; AU023367; add; PHS; PPDIV; PAPA1; PAPA; PAP-A; GLI3-190; GLI3FL; expressed sequence AI854843; Bph ... This deletion results in the expression of an abnormal transcript that fuses Gli3 sequences to an exon belonging to an apparent ... sequences 3 to exon 9, which includes sequences encoding some, but not all, of the zinc finger domains. ...
Coxsackievirus can persist in murine pancreas by deletion of 5′ terminal genomic sequences. J Med Virol. 11 August 2014 [Epub ... The viral genome was partially sequenced in all four virus-positive cases, and the sequence showed a perfect match with ... High-throughput sequencing of total RNA extracted from whole frozen tissue from each patient did not detect any viral sequences ... Sequencing confirmed that amplified sequences originated from enteroviruses.. The high sensitivity of PCR makes it susceptible ...
Additional primers were designed from either EDL933 or 86-24 genomic sequences to amplify and sequence regions upstream or ... The G+C content for the sequences shared among all isolates (Fig. 2a) was 51%, while that for the inserted sequence in strain ... Isolates G5295 and G5296 have a deletion in this region, resulting in the loss of the sequence containing the XbaI restriction ... Sequences that characterize mutational hot spots or other composition variations (20) were not observed in the sequences ...
... may result in genomic reaarangements such as deletions (left) or duplications (right) of intervening genomic sequences. g , 3′ ... a , Retrotransposon sequence (red box) can be recruited as coding sequence and integrated into a gene (made up here of two ... is sometimes associated with concomittant deletion of target genomic sequences (light blue box). f , Ectopic recombination ( ... a , Typical insertion of an L1, Alu or SVA retrotransposon (red box) at a new genomic site (blue area). If the new genomic site ...
Genomic science has made major technical leaps in recent years, most notably with the advent of next generation sequencing ... Phenotypic trait variation can be linked to genomic sequence variation. These differences range from a single nucleotide to ... larger insertion and deletion (indel) of chromosomal segments. Indels can change the copy number of affected genes, which can ... Background: One of the great advantages of next generation sequencing is the ability to generate large genomic datasets for ...
... the human sequences had 27 insertions and 22 deletions. Primer sequences for amplification of rhesus genomic CFTR sequences are ... Genomic DNA sequence of Rhesus (M-mulatta) cystic fibrosis (CFTR) gene MAMMALIAN GENOME Wine, J. J., Glavac, D., Hurlock, G., ... As part of a program to discover natural animal models for human genetic diseases, we have determined the genomic sequence of ... NEURAL MECHANISMS FOR SERIAL ORDER IN A STEREOTYPED BEHAVIOR SEQUENCE NATURE Reichert, H., Wine, J. J. 1982; 296 (5852): 86-87 ...
Alignment of the ESTs with the genomic sequence was further used to confirm AS. Alternatively spliced transcripts in each ... An insertion or deletion in the alignment of EST/EST was used to identify alternatively spliced transcripts. ... Methodology/Principal Findings A Basic Local Alignment Search Tool database was constructed for the expressed sequence tags ( ... The EST sequences were aligned first, compared with their genomic sequences, and then mapped onto chromosomes. These procedures ...
  • Whenever possible we will sequence whole genomes and in other cases use DNA capture methods to generate high-quality data from representative parts of the genome. (europa.eu)
  • The objective of this study was to present heritability estimates and accuracy of genomic prediction using different methods for meat quality traits in Nelore cattle. (bioportfolio.com)
  • Nucleic acid sequences are provided that are useful as amplification primers, hybridization probes, and as a portion of molecular beacon probes for amplifying and detecting polymorphisms of the β2 adrenergic receptor gene, compositions and kits incorporating the same, and methods employing the same. (google.com)
  • Increasingly detailed analyses of human and other primate genomes are revealing the scale and complexity of the past and current contributions of non-LTR retrotransposons to genomic change in the human lineage. (nih.gov)
  • Tandem mass spectrometry-mass spectrometry (MS/MS) analyses of the mutant peptides have revealed that both are shorter variants of 12S globulin with deletion sites detected within the alpha-subunits of 12S globulin cruciferin B (CRB) and C (CRC), respectively. (jove.com)
  • Sequence analyses of the genomic DNA flanking the deletion sites have demonstrated that both deletions occurred at the genomic level. (jove.com)
  • We present a cost-effective method for performing both DNA sequencing and methyl-seq from a single capture reaction thus reducing reagent costs, sample preparation time and DNA requirements for these complementary analyses. (biomedcentral.com)
  • The clinical molecular laboratory, which carries both CLIA and CAP accreditations, offers molecular genetics services such as DNA extraction, identification and validation of public and proprietary genetic variants, real-time PCR assay design and validation, Sangers sequencing with ABI3730xl high throughput instruments and customized clinical reporting. (operon.com)
  • Typical projects includeo DNA extraction, identification and validation of public and proprietary genetic variants, real-time PCR assay design and validation, Sangers sequencing with ABI3730xl high throughput instruments and customized clinical reporting. (operon.com)
  • The TaqMan Gene Copy Number Assay (Applied Biosystems) was used to verify the presence of gene deletions/multiplications. (hindawi.com)
  • A simple PCR assay using these Beijing/W strain-defining deletions will facilitate molecular epidemiological studies and may assist in the identification of the molecular basis of phenotypes associated with this important lineage of M. tuberculosis . (asm.org)
  • Furthermore, we present a method, based on Agilent SureSelect Methyl-Seq, that will use a single capture assay as a starting point to allow both DNA sequencing and methyl-seq. (biomedcentral.com)
  • Our method uses a single capture assay that is sequentially split and used for both DNA sequencing and methyl-seq. (biomedcentral.com)
  • The National Human Genome Research Institute (NHGRI) solicits Small Business Innovation Research (SBIR) grant applications from small business concerns (SBCs) that propose to develop novel technologies that will substantially reduce the cost of genomic DNA sequencing. (nih.gov)
  • Protein-coding sequences of DNA make up less than two percent of the human genome. (princeton.edu)
  • Studies designed to determine the sequence of the human genome, as well as studies designed to compare human genomic sequences, have elicited information regarding polymorphisms in the human genome. (google.com)
  • To map the location of CY17 more precisely, we isolated three yeast artificial chromosomes (YACs) containing CY17 that are present on the sequence tagged site (STS)-based map of the human genome ( 6 , 7 ). (sciencemag.org)
  • Our results further illustrate the instability of the ABCC6 genomic region and stress the importance of screening for deletions in the molecular diagnosis of PXE. (nature.com)
  • First, we are using microarray and next-generation high throughput sequencing to derive molecular signatures of young and old stem cells and the transcriptional and epigenetic levels. (stanford.edu)
  • 1. A composition comprising a molecular beacon probe for detecting a target sequence, the molecular beacon probe comprising a label moiety and a nucleic acid having a nucleotide sequence selected from the group consisting of SEQ ID NO: 6, SEQ ID NO:7, SEQ ID NO: 8, and SEQ ID NO: 9. (google.com)
  • No homozygous deletions of CY17 were detected in a panel of 65 breast tumor cell lines (25) and xenografts (40) ( 8 ), so eight additional markers were analyzed in the 10q23 region (D10S579, D10S215, AFMA086WG9, D10S541, AFM280WE1, WI-10275, WI-8733, WI-6971). (sciencemag.org)
  • Homozygous deletions of AFMA086WG9 were also detected in two of eight glioblastoma cell lines, three of 34 glioblastoma xenografts, and two of four prostate cancer cell lines ( 11 ). (sciencemag.org)
  • Multiplexing allows the simultaneous processing of many sequencing templates by pooling these at the earliest stages of the procedure and resolves them into individual sequences at the latest possible stage thus enabling a high throughput of templates with a reduction in repetitious steps. (harvard.edu)
  • Other improvements have come from comparing genomic DNA to cDNA sequences and analysis of RNASeq high-throughput data. (wikipedia.org)
  • In Drosophila, the sequencing of a single tumor caused by the loss of Polyhomeotic (Ph) revealed that neither single nucleotide polymorphisms (SNPs) nor copy number variations (CNVs) were significantly increased in comparison with non-tumoural control tissue, suggesting that genome instability (GI) may not be a pre-requisite for neoplastic epithelial growth in this model system. (g3journal.org)
  • We investigated the mechanisms for strain variation in O157 by recovering and examining nucleotide sequences flanking each of the Xba I restriction enzyme sites in the genome. (asm.org)
  • Strain EDL933 is the O157 isolate that has been sequenced at the University of Wisconsin-Madison ( 15 ). (asm.org)
  • The resultant genotype and epi-type data is highly comparable in terms of coverage and SNP/methylation site identification to that generated from separate captures for DNA sequencing and methyl-seq. (biomedcentral.com)
  • We found that 1024 transcripts did not represent any public human cDNA sequence and examined their expression using M. fascicularis oligonucleotide microarrays. (biomedcentral.com)
  • An insertion or deletion in the alignment of EST/EST was used to identify alternatively spliced transcripts. (plos.org)
  • Whereas deletion of RBP-J in renin-expressing cells of C57BL/6 mice leads to the development of B-cell leukemia, 129/SV mice develop dermatitis with a reactive, myeloproliferative phenotype. (biologists.org)
  • The phenotype of SNV carriers overlapped with that of 2p25.3 deletion carriers. (plos.org)