[Bioperl-l] Blast database sequence retrieval perl script

Hans Rudolf Hotz hrh at sanger.ac.uk
Tue Apr 8 08:48:32 EDT 2008


Nelson

or simply use the BLAST indices for the sequence retrieval as well.

All you need to do is adding the "-o" option to the 'formatdb' command for 
the BLAST index creation (this will create some extra files). Then you can 
use 'fastacmd' (which is also part of the NCBI BLAST package) to retrieve 
the sequences.


Hans

On Tue, 8 Apr 2008, Heikki Lehvaslaiho wrote:

>
> Dear Nelson,
>
> I am cc:ing the bioperl mailing list where all these kind of queries should
> go. More people can help you that way.
>
>
> Since you have your own local data set, you need to create an index that
> catalogues you sequences for easy retrieval.
>
> You need to install bioperl-live first. See for example:
> 	http://www.bioperl.org/wiki/Using_Subversion
>
> Then you can follow this HOWTO:
> 	http://www.bioperl.org/wiki/HOWTO:Flat_databases
>
> The other HOWTOs will help you dealing with BioPerl sequence objects that are
> retrieved: http://www.bioperl.org/wiki/HOWTOs.
>
>
> Yours,
>
> 	-Heikki
>
>
> On Monday 07 April 2008 14:50:23 Ndegwa, Nelson (IITA-Nairobi) wrote:
>> Dear Prof. Heikki,
>>
>> Hi. We met at the Pathogen Bioinformatics Conference held in Nairobi
>> Kenya in May 2007 at ICIPE. I recall you are a developer of Bioperl and
>> Perl. I have managed to install a local Blast, having just cowpea Contig
>> sequences, about 50,000 in total. This runs fine, as I can perform
>> various queries and get results. However, any good match/hit on the
>> local Blast database is hard to retrieve and the only option seems to go
>> back to that database and search manually for the top hit sequence - an
>> exceedingly manual task. Might you perhaps be having a Perl script I
>> could adopt to my database to help with this task Such that the hits
>> have a hyperlink which can be used to retrieve that specific entry? I
>> have limited knowledge of Perl. Thank you.
>>
>> With Kind Regards,
>>
>> Nelson.
>
>
>
> -- 
> ______ _/      _/_____________________________________________________
>      _/      _/
>     _/  _/  _/  Heikki Lehvaslaiho    heikki at_sanbi _ac _za
>    _/_/_/_/_/  Senior Scientist    skype: heikki_lehvaslaiho
>   _/  _/  _/  SANBI, South African National Bioinformatics Institute
>  _/  _/  _/  University of Western Cape, South Africa
>     _/      Phone: +27 21 959 2096   FAX: +27 21 959 2512
> ___ _/_/_/_/_/________________________________________________________
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
>


-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 


More information about the Bioperl-l mailing list