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The Reference Sequence (RefSeq) database [1] is an open access, annotated and curated collection of publicly available nucleotide sequences (DNA, RNA) and their protein products. RefSeq was introduced in 2000.
The sequence in brackets (GCC) is the motif with unknown biological impact. [5] There are variations within Kozak consensus sequence, such as G or A is observed three nucleotides upstream (at position -3) of AUG. Bases between positions -3 and +4 of Kozak sequence have the most significant impact on translational efficiency.
The NCBI assigns a unique identifier (taxonomy ID number) to each species of organism. [5] The NCBI has software tools that are available through web browsers or by FTP. For example, BLAST is a sequence similarity searching program. BLAST can do sequence comparisons against the GenBank DNA database in less than 15 seconds.
The EMBL Nucleotide Sequence Database (EMBL-Bank) has increased in size from around 600 entries in 1982 to over 2.5×10 8 by December 2012. [16] The EMBL Nucleotide Sequence Database (also known as EMBL-Bank) is the section of the ENA which contains high-level genome assembly details, as well as assembled sequences and their functional annotation.
The Cambridge Reference Sequence (CRS) for human mitochondrial DNA was first announced in 1981. [ 2 ] A group led by Fred Sanger at the University of Cambridge had sequenced the mitochondrial genome of one woman of European descent [ 3 ] during the 1970s, determining it to have a length of 16,569 base pairs (0.0006% of the nuclear human genome ...
Slider is an application for the Illumina Sequence Analyzer output that uses the "probability" files instead of the sequence files as an input for alignment to a reference sequence or a set of reference sequences. Yes Yes No No [53] [54] 2009-2010 SOAP, SOAP2, SOAP3, SOAP3-dp SOAP: robust with a small (1-3) number of gaps and mismatches.
An accession number, in bioinformatics, is a unique identifier given to a DNA or protein sequence record to allow for tracking of different versions of that sequence record and the associated sequence over time in a single data repository.
Having a reference genome around is convenient because then instead of storing the nucleotide sequences themselves, one can just align the reads to the reference genome and store the positions (pointers) and mismatches; the pointers can then be sorted according to their order in the reference sequence and encoded, e.g., with run-length encoding.