[Bioperl-l] StandAloneBlastPlus Question

[Chris Fields]

Using BLAST+ and makeblastdb, it seems as if the input files can be either FASTA or other BLAST databases, and it takes standard input.  You could try multiple -in parameters to see if it works (according to the BLAST docs this is supported).


>From 'makeblastdb':

 *** Input options
 -in <File_In>
   Input file/database name; the data type is automatically detected, it may
   be any of the following:
   	FASTA file(s) and/or 
   	BLAST database(s)
   Default = `-'
 -dbtype <String, `nucl', `prot'>
   Molecule type of input
   Default = `prot'


chris

On Apr 1, 2011, at 9:17 AM, Veronica A. wrote:

> Phew....I'm glad I'm not the only one :)
> 
> I'll look into the blastdb_aliastool method and see if that will help in the mean time.
> 
> Thank you.
> 
> Veronica
> 
> 
> 
>> From: David.Messina at sbc.su.se
>> Date: Fri, 1 Apr 2011 10:07:06 +0200
>> To: armendarez77 at hotmail.com
>> CC: bioperl-l at lists.open-bio.org; maj at fortinbras.us
>> Subject: Re: [Bioperl-l] StandAloneBlastPlus Question
>> 
>> Hi Veronica,
>> 
>> I took a look and couldn't figure out how to do an update to an existing
>> database, either. But I also couldn't find a clear example of how to do this
>> with just the blast+ command-line tools (outside of Perl).
>> 
>> Well, it looks like you can create a new, virtual database using
>> blastdb_aliastool. Is that what you mean? If not, could you provide an
>> example command line of how to update an existing blast database using the
>> blast+ command-line tools?
>> 
>> Also, Ccing Mark Jensen — he can probably answer this straight away.
>> 
>> 
>> Dave
>> 
>> 
>> 
>> 
>> 
>> On Fri, Apr 1, 2011 at 02:45, Veronica A. <armendarez77 at hotmail.com> wrote:
>> 
>>> 
>>> 
>>> 
>>> 
>>> Hello,
>>> 
>>> I'm trying to create a Perl script using StandAloneBlastPlus that can
>>> either create a new database or update it with new FASTA sequences.
>>> However, I can only find information on the creation of a new database.
>>> I've checked the information on doc.bioperl.org but a lot of the Methods
>>> don't have descriptions yet.
>>> 
>>> 
>>> Is it possible to use StandAloneBlastPlus or is there another/a better way?
>>> 
>>> Thank you,
>>> 
>>> Veronica
>>> 
>>> 
>>> 
>>> 
>>> 
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>> 
>> 
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