How? - Apply BLAST identities to transcriptome

[dacotahm]

Hello, I could use help with the following problem -

I've assembled a transcriptome and I can BLAST against Drosophila to identify some of the transcripts. Now I have two files: the BLAST output and transcript fasta. I would like to append the names (subject IDs) from the BLAST file to the fasta >headers.

The closest I can get is to format my BLAST output to a CSV with the query and subject IDs in the first two columns, but I'm not sure how to put together a script that will search for transcripts in my fasta and add the IDs.

Any advice or other solutions?

Thanks

[maubp]

Which scripting language are you learning? e.g. Perl, Python, or Ruby.

Whichever you pick, this should be a simple job combining the FASTA input file and the BLAST output to give an annotated FASTA file. BioPerl, Biopython or BioRuby would make it easy to work with the BLAST XML output, but I'd recommend the tabular output as it is trivial to parse.

[MeganS]

MAKER comes with an accessory script (maker_functional_fasta) that maps functional information onto a fasta. It might take some shuffling of your BLAST output to get it in the expected input format.

http://gmod.org/wiki/MAKER_Tutorial_2012#MAKER_Accessory_Scripts