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)
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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