Biopython Examples For Writing Genbank Files?

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11.9 years ago

Richard ▴ 590

Hi gang,

I have some sequences in Seq objects, and each has a corresponding list of interesting regions that I want to annotate in genbank format.

I imagine I need to use a SeqRecord object for each of my sequences if I want to write them (with annotations) to a genbank file.

Does anyone have a good example of how to properly setup a SeqRecord object such that I can easily create a genbank format file from it?

biopython genbank • 4.1k views

ADD COMMENT • link 11.9 years ago by Richard ▴ 590

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Yes, I would probably recommend creating a SeqRecord object (perhaps by loading a FASTA file), and adding a SeqFeature for each feature to appear in the GenBank feature table (from loading your list of regions).

Are you dealing with nice simple genes (e.g. bacteria) without introns? That makes life much easier.

ADD REPLY • link 11.9 years ago by Peter 6.0k

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Thanks Peter. I don't think I'm quite that lucky. I'm looking at antibody V,D,J assignment, so I'll need to annotate the parts of my sequence that are in the reference set (ie. pre-recombination).