Dear all,
I performed a blastx of some thousand contigs of size between 1500 and 5000 bp against uniref-protein database. To speed it up I set the following parameters:
-e 0.00001 -a 8 -b 1 -v 1
so I receive the best hit for each protein. But now I realized that I just got 1 match per contig but on my contigs I expect from NCBI blast 3 or more different hits for example from position on the contig A: 1 - 1000
B 1005 - 2500
C 2600 - 3100 ....... .
Does anybody know what parameter I have to set to get the different hits for A, B, C and so on and not only the 1 best hit of my contig?
Thanks in advance!
I performed a blastx of some thousand contigs of size between 1500 and 5000 bp against uniref-protein database. To speed it up I set the following parameters:
-e 0.00001 -a 8 -b 1 -v 1
so I receive the best hit for each protein. But now I realized that I just got 1 match per contig but on my contigs I expect from NCBI blast 3 or more different hits for example from position on the contig A: 1 - 1000
B 1005 - 2500
C 2600 - 3100 ....... .
Does anybody know what parameter I have to set to get the different hits for A, B, C and so on and not only the 1 best hit of my contig?
Thanks in advance!
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