PlasmidLab / Guides / Open a GenBank file
How to open a GenBank file (.gb, .gbk)
A GenBank file is plain text, so any text editor will show it to you. What a text editor will not show you is the map, which is the reason the file has features in it at all.
What is in the file
GenBank files end in .gb, .gbk, .gbff or .genbank and hold one or more records. Each record runs in this order:
- LOCUS, one line with the name, the length in base pairs, the molecule type, whether the sequence is circular or linear, and a date. For a plasmid this line is where "circular" is written down, and it changes how the map is drawn.
- DEFINITION, ACCESSION, VERSION, SOURCE, what the record is and where it came from.
- FEATURES, the annotations:
source,gene,CDS,promoter,rep_origin,misc_featureand others, each with a location and qualifiers such as/gene,/product,/noteand/translation. - ORIGIN, then the sequence in numbered blocks, and
//to end the record.
Reading a feature location
1..100 is bases 1 to 100 on the top strand. complement(200..300) is the same stretch read on the bottom strand, which is how a gene pointing the other way is written. join(2600..2686,1..50) is one feature in two pieces, which is also how a feature that crosses the origin of a circular plasmid is written.
Open it
Install PlasmidLab, then choose File > Open… or drop the file on the window. The sequence, the features and the circular or linear map open together, and the file can be edited and saved again. The same works for FASTA, EMBL and SnapGene® .dna files; the file-opening guide lists the formats.
Fetch one by accession
Choose File > Get from NCBI… and type an accession, for example L09137 for pUC19. File > Get from Ensembl… and File > Browse Addgene do the same for those two sources. These lookups send the accession you typed over the internet; everything else stays on your computer.
Save it as something else
File > Save As… writes GenBank, FASTA or .dna, so a GenBank file from a collaborator can go back out in whatever format the next person needs.