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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 extensible NEXUS file format is widely used in bioinformatics.It stores information about taxa, morphological and molecular characters, distances, genetic codes, assumptions, sets, trees, etc. [1] Several popular phylogenetic programs such as PAUP*, [2] MrBayes, [3] Mesquite, [4] MacClade [5] and SplitsTree [6] use this format.
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.
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Sequence Alignment Map (SAM) is a text-based format originally for storing biological sequences aligned to a reference sequence developed by Heng Li and Bob Handsaker et al. [1] It was developed when the 1000 Genomes Project wanted to move away from the MAQ mapper format and decided to design a new format.
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.
EzTaxon-e: database for the identification of prokaryotes based on 16S ribosomal RNA gene sequences; NCBI Taxonomy: a taxonomic database operated by NCBI and concentrating on all taxa for which DNA sequences are available (those sequences are stored by GenBank, another database operated by NCBI).
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.