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Old 07-29-2013, 05:22 PM   #1
mcbaindesu
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Default One result per line for blastp?

Hi all,

I am trying to annotate a long list of orfs by blasting the translated aa sequences against a local uniprot_sprot database. I am using the blast+ version of blastp.

I want at least one line per query sequence with output format 6. In some cases it is not possible to get a single result line per query (sometimes you get multiple HSPs returned even when using -max_target_seqs 1). But I have found solutions to that problem. (You need to remove extra lines using sort -u, there is a thread about it here: http://seqanswers.com/forums/archive...p/t-27735.html)

The problem is that if there is no significant hit, no result is returned for that particular query sequence, so the output file is missing some lines. Is there a way to force blastp to give me a result per line?? 'No significant similarity' in the sseqid column would be suitable for example.

(Basically I am trying to make it as easy as possible to add annotation columns to my tab-delimited file of ORFs)
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Old 07-30-2013, 02:41 AM   #2
rhinoceros
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Default

I'm not sure, but maybe -outfmt 7 (tabular with comment lines) reports also non-hits..
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Old 08-01-2013, 05:07 PM   #3
mcbaindesu
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Default

Thanks for the reply, I think you are correct, -outfmt 7 will probably give a result with comment lines for queries without hits.

It would still need post-processing to incorporate it into my database and I think the -outfmt6 files will be easier for a novice like me to process.

Basically either way I need to learn the basic unix text processing tools! (it will be better for me in the long run to do that rather than keep on using vlookup in excel! )

Here are some realted threads:
http://seqanswers.com/forums/showthread.php?t=21524
http://seqanswers.com/forums/showthread.php?t=14498
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