How to Read a GenBank File

The header

• LOCUS: the name, the length in base pairs, the molecule type (DNA, mRNA), whether it is linear or circular, and a date.
• DEFINITION: a one-line description.
• ACCESSION and VERSION: the record's ID, such as NM_000546.6. The number after the dot changes when the sequence changes.
• SOURCE and ORGANISM: where the sequence comes from.
• REFERENCE: the papers that describe it.

FEATURES

Each feature has a type (gene, CDS, promoter, misc_feature) and a location, followed by qualifiers such as /gene="TP53", /product= or /translation=, which holds the protein sequence of a CDS.

• 100..500: bases 100 to 500 on the top strand.
• complement(100..500): the same bases, read on the opposite strand.
• join(100..200,300..450): pieces joined together, such as the exons of a gene.
• <1..300 or 200..>900: the feature carries on past the end of the sequence.

ORIGIN

The sequence itself, in lowercase blocks of ten with the position at the start of each line, ending with //.

Working with it

The GenBank to FASTA converter strips the numbers and spaces and gives the plain sequence that most tools expect. To see the features drawn as a map, open the file in the Plasmid Map Viewer. A feature on the complement strand reads 5' to 3' as the reverse complement of its range.