Extracting unique BLAST hits from a multi-hit region

[thmourikis]

Hi all,

I have a blast output file (from BLAST command line tool) and I want to extract from it the unique hits. I have several genomic regions of variable size and I explore them using BLAST against a home made database (there is redundancy in it). What I want to get out is one hit per fragment of the examined region. Any suggestions? I am using perl, so any answers using BioPerl would be highly appreciated.

Thanks a lot in advance.
Thanos

[rhinoceros]

If you used tabular output, it would be rather trivial to parse it with cut and sort and then retrieve the sequences from your db with blastdbcmd..

[thmourikis]

Hi rhinoceros and thanks a lot for your immediate response. By tabular output do you mean option 6 in the -outfmt flag?

I will try what you suggested, seems indeed fairly simple.

Thanks once again,
Thanos

[rhinoceros]

Yeah, -outfmt 6

Also, have a look here. It's probably rather relevant (second post)

[thmourikis]

Thanks a lot once again for your help. I really appreciate that.

[thmourikis]

Do you probably know how I can add subject description in the tabular output? I need them for the next steps in my pipeline. :-)

Thanks in advance.

[rhinoceros]

Have a look at the manual

syntax would be e.g. -outfmt '6 std stitle'

However, since your db is not provided by ncbi, this will not work (or so I'd reason). Anyway, if you created your db with -parse_seqids and the descriptions are stored there in the headers, you can just take the hits from your blast and retrieve the sequences and descriptions with blastdbcmd.

cut -f 1 yourTabOutput | sort -u > id_list (or maybe it's cut -f 2..)
blastdbcmd -entry_batch id_list ..etc

[thmourikis]

Thank you once again for your response rhinoceros. I will go through it right now and check the option you suggested.