Question: Number of Blast hits for multiple sequence fasta
0
gravatar for mosquitoes
4.3 years ago by
mosquitoes0
United States
mosquitoes0 wrote:

Using command line blast v. 2.2.31+ the neither of the following commands will return only 2 subjects per query:

blastn -query multiple_sequences.fa -db database -task blastn -dust no -outfmt "7 std" -max_target_seqs 2 -out outputfile
blastn -query multiple_sequences.fa -db database -task blastn -dust no -outfmt "7 std" -num_alignments 2 -out outputfile

There are a few posts about this, but none related to submitting with multiple sequences in the fasta. Any ideas why these commands do not work for only outputting two subject sequences per query?

blast • 1.4k views
ADD COMMENTlink modified 3.9 years ago by Biostar ♦♦ 20 • written 4.3 years ago by mosquitoes0

Look for this command; I think it is.

-max-hsps 2
ADD REPLYlink written 2.7 years ago by Buffo1.7k
0
gravatar for Lesley Sitter
4.3 years ago by
Lesley Sitter490
Netherlands
Lesley Sitter490 wrote:

Hi,
Just found this link;
http://seqanswers.com/forums/archive/index.php/t-27735.html

Seems it has something to do with HSP? Although i can't find any additional information about this om the NCBI site itself.
Also maybe you would want to try outfmt 6, it does not have any comment lines which makes it easier to parse (then you can just create a small script or awk argument that only takes the first hit)

ADD COMMENTlink written 4.3 years ago by Lesley Sitter490
2

As far as I know, max_targets looks at the number of matched sequences, not the number of actually produced hits. Meaning, if you have multiple hits to the same sequence (say an entire chromosome) this still only counts as a single hit on the target.

ADD REPLYlink written 4.3 years ago by thackl2.7k
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