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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.
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Note that more recent versions of Illumina software output a sample number (defined by the order of the samples in the sample sheet) in place of an index sequence when an index sequence is not explicitly specified for a sample in the sample sheet. For example, the following header might appear in a FASTQ file belonging to the first sample of a ...
This allows a sequence that was obtained from a database to be labelled with a reference to its database record. The database identifier format is understood by the NCBI tools like makeblastdb and table2asn. The following list describes the NCBI FASTA defined format for sequence identifiers. [9]
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.
Protein sequence databases PROSITE: database of protein families and domains: Protein sequence databases Protein Information Resource: Georgetown University Medical Center [GUMC] Protein sequence databases SUPERFAMILY: library of HMMs representing superfamilies and database of (superfamily and family) annotations for all completely sequenced ...
The 1-based position of the variation on the given sequence. 3: ID: The identifier of the variation, e.g. a dbSNP rs identifier, or if unknown a ".". Multiple identifiers should be separated by semi-colons without white-space. 4: REF: The reference base (or bases in the case of an indel) at the given position on the given reference sequence. 5: ALT