NCBI

Genbank is a publically accessible flat file database structure for primary nucleotide sequence information and auxillary information. The amount of information publically submitted has been growing exponentially. In August 2005 this DNA sequence database reached 100 gigabases. These records can display the ORIGIN information for different nucleotide molecular types, and have no limit on the length of sequence displayed. Entire chromosomes can be stored as a genbank record for an organism of interest, potentially making the disk storage of the record very large.

An example Genbank sample record (U49845 actual Genbank record)

Regular expressions matching parts we care about

Genbank

• The unique ACCESSION number
• The ORIGIN field
• Any amino acid /translation field in the FEATURE table

FASTA

There is a condensed file format called a FASTA format is used to manipulate primary sequence information. FASTA files can be nucleotide or amino acid records. the first row of the record starts with a > and can contain any description information about the record. It is recommended that all lines of text be shorter than 80 characters in length.

An example of an amino acid FASTA record, in this case the description information is a consise format separated by pipe characters |. The second field is the ACCESSION number refering to the amino acid GENPEPT record.

>gi|[http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&val=532319 532319]|pir|TVFV2E|TVFV2E envelope protein
ELRLRYCAPAGFALLKCNDADYDGFKTNCSNVSVVHCTNLMNTTVTTGLLLNGSYSENRT
QIWQKHRTSNDSALILLNKHYNLTVTCKRPGNKTVLPVTIMAGLVFHSQKYNLRLRQAWC
HFPSNWKGAWKEVKEEIVNLPKERYRGTNDPKRIFFQRQWGDPETANLWFNCHGEFFYCK
MDWFLNYLNNLTVDADHNECKNTSGTKSGNKRAPGPCVQRTYVACHIRSVIIWLETISKK
TYAPPREGHLECTSTVTGMTVELNYIPKNRTNVTLSPQIESIWAAELDRYKLVEITPIGF
APTEVRRYTGGHERQKRVPFVXXXXXXXXXXXXXXXXXXXXXXVQSQHLLAGILQQQKNL
LAAVEAQQQMLKLTIWGVK

(U49845 actual FASTA record)

See also

• NCBI GenBank Overview
• Template:extension (template code constructor)
• Extension:Example (working example)