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Table 2 Atlas toolbox applications.

From: Atlas – a data warehouse for integrative bioinformatics

Application Function Input Output
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)