[Bioperl-l] remove overlapped sequences from Blastn results

[Chris Fields]

Marcelo,

(Make sure to keep responses on the main list)

The new Tiling stuff is in bioperl-live (subversion code); it hasn't  
been released yet but should appear in BioPerl 1.6.1 (an alpha will be  
out this week).

chris

On Sep 2, 2009, at 3:20 PM, Marcelo Iwata wrote:

> thanks Chris.
> I was at cpan search to download Bio::Search::Tiling, and it returns  
> to me the bioperl core module:
> BioPerl-1.6.0.tar.gz
> at http://search.cpan.org/~cjfields/BioPerl-1.6.0/Bio/Search/BlastStatistics.pm
>
> i've downloaded and upgrade my bioperl version, but, still not find  
> the MapTiling.pm
>
> Could this be result of Some kind of error at upgrade?
>  thks.
>
>
> On Tue, Sep 1, 2009 at 3:10 PM, Chris Fields <cjfields at illinois.edu>  
> wrote:
> 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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