03 January 2014

BLAST and blast2GO

Next post Previous post

Friday Jan 3

ApTranscriptome

Running test of b24gpipe on subsample of first 99 sequences from AphVTsub18_blastx2nrinsecta.xml. Note that I had to add

</BlastOutput_iterations>
</BlastOutput>

to end of xml file so it would be imported correctly.

Test run took 39min to complete. Not going to be feasible to do this for entire transcriptome…about 10 days for each 5k sequence blast xml file!!

Checked googlegroups and biostars for alternatives. Seems that a local install of blast2go database would speed this up, but unclear if by enough to make worthwhile.

Alternative would be to modify SFG total_annotation.py script to work with only NCBI results…