[Bioperl-l] Fwd: megablast using bioperl

[Chris Fields]

Acc. to the blastall docs MEGABLAST is just setting -n to T for blastall.  Is that what you mean?

pyrimidine1:~ cjfields$ blast-2.2.22/bin/blastall -

blastall 2.2.22   arguments:

  -p  Program Name [String]
  -d  Database [String]
    default = nr
...
  -n  MegaBlast search [T/F]
    default = F

chris

On Feb 1, 2010, at 2:38 PM, Xiujing Gu wrote:

> Thanks for the links!
> But, they only talk about the regular blastall program, not the megablast.
> 
> I am not sure how can I switch from blastall to megablast. I tried to just call megablast, but I got a very differenct report.
> 
> $VAR1 = bless( {
>                  'primary_seq' => bless( {
>                                            'display_id' => 'test',
>                                            '_seq_length' => undef,
>                                            '_root_verbose' => 0,
>                                            'seq' =>
> 'TGAACCTAGAAGTATTTGTTGCTGGGTTTGTCTTCAGGTTCTGTTGCTCGGTTTTCTAGTTCCCCACCTAGTCTGGGTTACTCTGCAGCTACTTTTGCATTACAATGGCCTTGGTGAGACTGGTAGACGGGATTAACTGAGAATTCACAAGGGTGGGTCAGTAGGGGGTGTGCCCGCCAGGAGGGGTGGGTCTAAGGTGATAGAGCCTTCATTATAAATCTAGAGACTCCAGGATTTTAACGTTCTGCTGGACTGAGCTGGTTGCCTCATGTTATTATGCAGGCAACTCACTTTATCCCAATTTCTTGATACTTTTCCTTCTGGAGGTCCTATTTCTCTAACATCTTCCAGAAAAGTCTTAAAGCTGCCTTAACCTTTTTTCCAGTCCACCTCTTAAATTTTTTCCTCCTCTTCCTCTATACTAACATGAGTGTGGATCCAGCTTGTCCCCAAAGCTTGCCTTGCTTTGAAGCATCCGACTGTAAAGAATCTTCACCTATGCCTGTGATTTGTGGGCCTGAAGAAAACTATCCATCCTTGCAAATGTCTTCTGCTGAGATGCCTCACACGGAGACTGGTAAGAAAGAAATTTATCCTTGAAAGGCCAAGTTCCTTAAGGGAAAAGAGAGAAGGAGAGAGGGTTAAGGGATCATTTCCCTCTTGAGCAATGATGGACCATTACTATAAAGAAGTGTTATTATCAACTAATCCTCTGGAAACCCCTTTTTCCATTATAACTTGGTGGCACCTGCCCTTTGAACTATGTCCCAGGTCTCAGGAGTGTGCATTGAGTTGAAGGACACAGAATTCGGCAGTTGAACAGTGTGCAGTAAGTTTGAGAACCTATGGGCTTAGGCATGGTGGAAACAAAAATGTATCGTTATAGTTAAATGAAGGTGATGTGTACATCTTCACATAGTGCTGGACACATGTGAATAAATAGCAGATTTATTGCTAATTAGCCA
> GAAGACCTAACGTCATAGCTCAGGGATGAGCATGATTTTGTTTTGCCAAAAATGGCATGGCAAATCACGATGAGATTTCTGTAATACATAATTTGGGTAATTCTTTCTATGTCAGTAACGGCTGTCTCTTCTCCATTCTCTGGGTTTGTGGATGTTACTGGGCAGCTCTGAGTTTGGGAGCACCTCCCATGTCTAATTCTCCTAAGTCCTGGGAAGCGTTGACCCAACTTTATGGTAAAGATAATTCCAGAAAGTTTAATCTACTGACAGTCAAACAGAATGTAGCTAGAAGTCCAGTTTGGCTTCAAAACCTGTGCTAGTACTCATGCTTCTGACTGGTAGCTGCAAGGGGTGGGGGATACTCGGGATACTCATAAAGCCGCTACCACTTTTTTGAAAATCAATTTTTCAGTAGTTTTCAAAAACTTGAGAATGAACCAACTTTACCAAGAATG',
>                                            'alphabet' => 'dna'
>                                          }, 'Bio::PrimarySeq' ),
>                  '_root_verbose' => 0
>                }, 'Bio::Seq' );
> Can't locate object method "nextSbjct" via package "Bio::Seq" 
> 
> 
> 
> Thanks,
> Xiujing Gu
> 
> 
> --- On Mon, 2/1/10, Smithies, Russell <Russell.Smithies at agresearch.co.nz> wrote:
> 
> From: Smithies, Russell <Russell.Smithies at agresearch.co.nz>
> Subject: RE: [Bioperl-l] Fwd: megablast using bioperl
> To: "'BioPerl List'" <bioperl-l at lists.open-bio.org>
> Cc: "'xiujingg at yahoo.com'" <xiujingg at yahoo.com>
> Date: Monday, February 1, 2010, 3:12 PM
> 
> Have you read the docs? It's very well documented:
> http://search.cpan.org/~cjfields/BioPerl-1.6.1/Bio/Tools/Run/StandAloneBlast.pm
> 
> Have you searched the BioPerl wiki? Again, well documented with examples:
> http://www.bioperl.org/wiki/HOWTO:StandAloneBlast
> 
> And if that doesn't help, perhaps you need to improve your Google skills:
> http://www.google.com/support/websearch/?ctx=web
> 
> --Russell
> 
> 
> 
>> -----Original Message-----
>> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
>> bounces at lists.open-bio.org] On Behalf Of Jason Stajich
>> Sent: Tuesday, 2 February 2010 8:48 a.m.
>> To: BioPerl List
>> Cc: xiujingg at yahoo.com
>> Subject: [Bioperl-l] Fwd: megablast using bioperl
>> 
>> Xiujing -
>> Your message is best asked on the mailing list.
>> 
>> Begin forwarded message:
>> 
>>> From: Xiujing Gu <xiujingg at yahoo.com>
>>> Date: February 1, 2010 7:58:55 AM PST
>>> To: jason at bioperl.org
>>> Subject: megablast using bioperl
>>> 
>>> Hello Jason:
>>> 
>>> After numerous googling, I found you might be the only person who
>>> knows about this subject. Would you so kindly show me an example of
>>> setting up megablast using bioperl Bio::Tools::Run::StandAloneBlast?
>>> 
>>> Thanks a lot!
>>> 
>>> Best regards,
>>> Xiujing
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
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