Creating Embl File Using Biopython - Genome Annotation

Question

[jcastrofigueroa]

Hello: I need help! I'm trying to do the annotation of a genome of a microbe using BioPython. I have already identified the ORFs (RAST), their putative function (BLAST), conserved domains of the proteins encoded in the genome (RPS-BLAST), etc., but all this information is separated into different .xml files and I would like to merge all the information, automatically, into one single *.embl file and I want it to be readable by Artemis, for example. I don't know how to do this, please I need some good guidelines to start with.

Cheers!

JCF

[jcastrofigueroa]

I've found out that I need to write the information in GFF3 format to be readable by Artemis. Does anyone have more Ideas? - thanks

Answer 1

[Peter]

That is possible using Biopython to write EMBL or GenBank files which can be loaded into Artemis. You need to make an annotated SeqRecord object whose features list is populated with SeqFeature objects (see the Biopython Tutorial), and then call SeqIO.write to save it to a file.

[jcastrofigueroa]

Hello: I think I have some problems with the annotation and here are some inquiries:

1. How can I add the parent DNA sequence to my annotation file? - I mean the source sequence.

2. How can I add a to my coding sequence (feature.type='CDS') the translate sequence of it?

Thanks

[Peter]

1. Create a SeqRecord object with its .seq populated using the DNA sequence as a Seq object.

2. Create a SeqFeature object of type CDS with a translation entry in the qualifiers dictionary.

Basically trying parsing some existing EMBL files and then mimic the structure used.

[jcastrofigueroa]

Thanks for your answer