Table 2 Atlas toolbox applications.

Sequence

ac2seq

Retrieve sequences given an accession

Nucleic acid or Protein Accession Number(s)

Sequences in Fasta format

feat2seq

Retrieve sub-sequences that span features

Feature type (and qualifier)

Sequences in Fasta format

gi2seq

Retrieve sequences given a GenInfo identifier

GenInfo Identifier(s) (GI Number(s))

Sequences in Fasta format

gi2seqentry

Retrieve sequences given a GenInfo identifier

GenInfo Identifier(s) (GI Number(s))

GBFF, EMBL, GFF, FTABLE, ASN.1, GBSEQ

tax2seq

Retrieve sequences by taxonomy

NCBI taxon identifier or scientific name of taxon

Sequences in Fasta format

tech2seq

Retrieve sequences by sequencing technique

Sequencing technique (eg EST, GSS, etc.)

Sequences in Fasta format

techtax2seq

Retrieve sequences by taxonomy and sequencing technique

Sequencing technique and NCBI taxonid/scientific name of taxon

Sequences in Fasta format

Loader

fastaloader

Fasta sequence data loader

Sequences in Fasta format

seqloader

ASN.1 sequence data loader

GenBank/RefSeq ASN.1 records

Feature

ac2feat

Retrieve features

GenBank Accession number (s)

Features in GFF or FTABLE format

gi2feat

Retrieve features

GenInfo Identifier(s) (GI Number(s))

Features in GFF or FTABLE format

Taxonomy

ac2tax

Retrieve taxonomy given an accession number

GenBank Accession number (string)

NCBI taxon identifier (integer)

gi2tax

Retrieve taxonomy given a GenInfo identifier

GenInfo Identifier (integer)

NCBI taxon identifier (integer)

ID Converters

ac2gi

Convert an accession number to a GenInfo identifier

GenBank Accession number (string)

GenInfo Identifier (integer)

gi2ac

Convert a GenInfo identifier to an accession number

GenInfo Identifier (integer)

Accession number (string)

tax2gi

Retrieve GenInfo identifiers associated with taxon identifier

NCBI taxon identifier (integer)

GenInfo Identifier (integer)