[NCBI BLAST] MAKE Limitation of BLAST Results.

Question

[clear.choi]

Hello,

I am using blast version ncbi-blast-2.2.29+.

I wonder how I can make limitation of alignment information per allele

For Example as below,

If blast search results like below,

> AI4E8.UA
Length=130

Score = 99.0 bits (53),  Expect = 2e-22
Identities = 53/53 (100%), Gaps = 0/53 (0%)
Strand=Plus/Plus

Query  3012  AGGCAAGATTTGTTCCTGCCCTTCTACGATGTGATGCTTGCACAAGTGATCCA  3064
             |||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  78    AGGCAAGATTTGTTCCTGCCCTTCTACGATGTGATGCTTGCACAAGTGATCCA  130

Score = 56.5 bits (30),  Expect = 1e-09
Identities = 30/30 (100%), Gaps = 0/30 (0%)
Strand=Plus/Plus

Query  17  GCAGTCGAACATGTAGCTGACTCAGGTCAC  46
           ||||||||||||||||||||||||||||||
Sbjct  1   GCAGTCGAACATGTAGCTGACTCAGGTCAC  30

Score = 56 bits (30),  Expect = 1e-09
Identities = 29/29 (100%), Gaps = 0/30 (0%)
Strand=Plus/Plus

Query 1000  GCAGTCGAACATGTAGCTGACTCAGGTCA  1029
           |||||||||||||||||||||||||||||
Sbjct  45   GCAGTCGAACATGTAGCTGACTCAGGTCA  74

There are three information, However, I would like bring only top two score from above Allele > AI4E8.UA.

I found some parameter which is -num_alignments, -num_descriptions , -max_target_seqs But those are not directly related with that.

Is there any specific parameter for that? Thank you,

[Jenez]

However, I would like bring only top two score from above Allele > AI4E8.UA.

Could you clarify what it is you want to achieve? Not sure I understand you... Do you want the top two scores only or do you want the above mentioned output just excluding the third alignment?

[clear.choi]

@Jenez Sorry for confusing you, Yes It is! I would like to bring only two alignment information excluding the third alignment.

[John Torcivia]

If you add the argument -num_alignments 2 that should restrict it to just 2 alignment results. That didn't work for you?