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PDF Bioinformatics Glossary FR3 Bioinformatics Primer v1 June 23, 2014 FR3 Bioinformatics Primer: Glossary of terms* (*from various sources including Discovering Genomics, Proteomics, & Bioinformatics 2nd edition, Campbell and Heyer; The Internet and the New Biology by Peruski and Peruski; and Bioinformatics for Dummies by Claverie and Notredame) Accession number identification Antisense technology molecular number given to every DNA and method that uses a nucleic acid protein sequence submitted to NCBI sequence complementary to an or equivalent database. mRNA so that the two bind and the mRNA is effectively neutralized. Algorithm step-by-step procedure for solving a problem (e.g. aligning Array an orderly pattern of objects. two sequences) or computing a In genomic studies, there are quantity (e.g. %GC). Typically microarrays and macroarrays. written in Perl or another computer Microarrays are small spots of DNA language. or protein and the identity of the spotted material is known. Alignment representation of two or Macroarrays are bacterial, yeast or more protein or nucleotide similar colonies on plates used to sequences where identical amino determine functional consequences acids or nucleotides are in the same of genomic manipulations. columns while missing amino acids or nucleotides are replaced with Anonymous FTP A file transfer gaps. protocol (FTP) that allows the retrieval of files from public sites. Allele frequency prevalence of a gene variant in a population. Archive a collection of data, text, programs or other electronic Annotate a genome is annotated information stored for other parties to once it has been analyzed for gene access or retrieve, typically without content. A gene is considered charge. annotated if it has been assigned information pertaining to a cellular ASCII stands for American Standard role. Code for Information Interchange, sets a unique numeric definition for Antibody array An antibody each of the most commonly used microarray is a specific form of characters in Western language, protein microarrays, a collection of including numerals, letters and some capture antibodies are spotted and symbols. An ASCII set is these fixed on a solid surface such as characters and their numbers. In the glass, plastic or silicon chip, for the context of a file, an ASCII file is one purpose of detecting antigens. that contains only text characters: 1 FR3 Bioinformatics Primer v1 June 23, 2014 numbers, letters and standard punctuation. Bootstrap analysis a statistical technique used to assess the Bacterial artificial chromosome reliability of the branching structure (BAC) cloning vector replicated in in phylogenetic trees. bacteria that can hold an insert of about 150,000 base pairs. Bowtie software that maps short DNA sequences to a reference BAM file a binary version of a SAM genome. file, the format is .bam. Browser client software that reads BankIt a computer program HTML-formatted documents and developed by the NCBI for displays them on your computer submitting your own sequences to screen. GenBank. cDNA, see complementary DNA Binomial a probability model for counting the number of ‘successes’ CDS acronym for ‘coding sequences’ in an experiment with two possible outcomes. Cellular component a term coined by Gene Ontology to describe Bioinformatics a field of study that subcellular structures, locations and extracts biological information from macromolecular complexes such as large data sets such as sequences, nucleus, telomere, and mitotic protein interactions, microarrays, etc. spindles. This field also includes the area of data visualization. ChIP-Seq, chromatin immunoprecipitation sequencing Biological process coined by Gene combination of chromatin Ontology to describe broad cellular immunoprecipitation and massively outcomes, such as mitosis or energy parallel sequencing used to survey production, that are accomplished by interactions between protein, DNA ordered assemblies of molecules. and RNA. BLAST the protein and nucleic acid Chromatogram a four-colored graph sequence search engine developed produced from nonradioactive at NCBI that allows you to search dideoxy sequencing methods sequence databases. BLASTn including cycle sequencing. searches for nucleotide sequences, BLASTp searches for amino acid Clade group of related species and sequences; BLAST2 compares 2 their common ancestors. sequences. Cladogram phylogenetic tree BLOSUM, block scoring matrix, a showing the relationship between the popular substitution matrix for species. aligning protein sequences. 2 FR3 Bioinformatics Primer v1 June 23, 2014 Client In its simplest form a client is Conserved domain (CD) a domain a software program that an individual that has been retained during uses to send requests to a server. In evolution presumably due to its a broader definition it can mean a essential role within the protein’s computer or computer program that structure. Conserved domain requests a service of a host searches are a part of the BLAST computer or program. search. Clone noun or verb. A clone is any Constitutive always active; molecule/cell/organism present in constitutive promoters or genes are more than one identical copy. To active at all times. clone something means to produce more than one copy of the original Contiguous (contigs) overlapping molecule/cell/organism. DNA segments that as a collection form a longer and gapless segment ClustalW the most popular program of DNA. for making multiple sequence alignments. Correlation coefficient a measure of the correspondence between two Clustering action of grouping sets of data. sequences according to their similarity Covariance analysis the study of a sequence that follows the evolution Clusters of orthologous groups of two different positions and looks COG NCBI compilations of for some correlation. evolutionarily related gene sequences from several microbial Coverage based on the number of genomes. This site allows you to bases sequenced in a genome, the search by gene or cellular role and coverage represents how many produce dendrograms to show times an average base was sequence similarities. sequenced; finished genomes frequently have 8X coverage. Comparative genomics analysis based on comparisons of entire Cufflinks software that accepts genomes. aligned RNAseq reads and estimates the relative abundances of Complementary DNA abbreviation transcripts. Also tests for differential used at NCBI to indicate which expression between samples. bases constitute the open reading frame. Cy3 and Cy5 fluorescent green and red dyes, respectively, that are Consensus a pseudo sequence commonly used for microarray where each residue summarizes experiments. (using the majority rule) the content of a column in a multiple sequence Curate oversee/annotate/manipulate alignment. gene data (often manually). Includes 3 FR3 Bioinformatics Primer v1 June 23, 2014 fine annotation of genes, filtering of Draft sequence a description of the genes according to certain degree of confidence in a DNA parameters and construction and sequence. When the DNA has been manipulation of gene models. sequenced only 4 times it is described as a ‘draft sequence’ as Dendrogram another name for opposed to a ‘finished sequence’ phylogenetic tree. The ClustalW which has been sequenced 8 times. guide tree is often referred to as a With a draft sequence about 95% of dendrogram, it is a file with a .dnd the genes should be identifiable. extension. dsDNA double stranded DNA, Distance matrix matrix that contains formed when two complementary all the pairwise distances between DNA sequences bind each other. sequences in a data set. Distance matrices afe often u sed to compute dsRNA double stranded RNA, phylogenetic trees. Not a formed when two complementary substitution matrix. RNA sequences bind to each other. DNA microarray or DNA chip E value (Expect value) when synonyms for gene sequences performing a BLAST search, you will spotted on glass slides used to obtain an E-value for each sequence measure simultaneously the level of that is retrieved. An E-value can be transcription of many genes. thought of as the probability that two sequences are similar to each other Domain (computational) a network by chance. Therefore E-values are or portion thereof that operates best when they are small (e.g. 1 x under a single administrative 10-12). umbrella such as an institution, a group of institutions, a geographical EC number, Enzyme Commission region, or a country. number a numerical classification scheme for enzymes based on the Domain (molecular) a protein unit chemical reactions they catalyze. of at least 50 amino acids that can fold on its own, can also be used for EBI, European Bioinformatics protein sequences that occur in Institute the European counterpart various contexts. to the NCBI in the U.S. Dot matrix dot plot, a method for EMBL, European Molecular representing the similarity between Biology Laboratory, this acronym two sequences without using an refers to the nucleotide database alignment. that the laboratory maintains. Downstream a relative direction for Entrez the NCBI database querying a DNA sequence; towards the 3’ system that is similar to SRS at the end. EBL. 4 FR3 Bioinformatics Primer v1 June 23, 2014 Epitope a part of an antigen that is commend method of transferring recognized by the immune system. files across networks and between remote computers. EST, expressed sequence tag a short subset of a cDNA sequence. GA II Illumina sequencing platform that generates 40 Mb sequence per Expansionist a person who takes a run with paired read lengths
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