[Bioperl-l] remove overlapped sequences from Blastn results

[Chris Fields]

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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