[Bioperl-l] remove overlapped sequences from Blastn results
Chris Fields
cjfields at illinois.edu
Tue Sep 1 18:10:30 UTC 2009
Marcelo,
Do you mean tiling? See:
http://www.bioperl.org/wiki/HOWTO:Tiling
chris
On Sep 1, 2009, at 12:33 PM, Marcelo Iwata wrote:
> Hi
>
> I've made a blastn with such arguments:
>
> ../bin/blastall -p blastn -d DBBank -i myFasta.FASTA.txt -e 0.00001
> -o
> Out2Blast.txt -a 8
>
> and i want a script that removes overlapped sequences from the
> results..
> For example, if a unigene A has the hit->start and hit-end as 1 and
> 4, and
> the B is at 2 and 3, respectively, the script remove second one.
>
> I want to know if it already exist, and if not, is there a library
> that
> works with such issue.
>
> I know that at Bio::DB::gff we have overlapping_features. But , if
> something
> directly exist (works with blast format), is better for me.
>
> thanks in advance
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