[Bioperl-l] Fwd: megablast using bioperl

[Smithies, Russell]

I don't think it allows a discontiguous template when run via blastall though.
"blastall -p blastn -n T"  will give you a different result than straight megablast.

--Russell

> -----Original Message-----
> From: Chris Fields [mailto:cjfields at illinois.edu]
> Sent: Tuesday, 2 February 2010 11:03 a.m.
> To: Xiujing Gu
> Cc: 'BioPerl List'; Smithies, Russell
> Subject: Re: [Bioperl-l] Fwd: megablast using bioperl
> 
> 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' =>
> >
> 'TGAACCTAGAAGTATTTGTTGCTGGGTTTGTCTTCAGGTTCTGTTGCTCGGTTTTCTAGTTCCCCACCTAGTC
> TGGGTTACTCTGCAGCTACTTTTGCATTACAATGGCCTTGGTGAGACTGGTAGACGGGATTAACTGAGAATTCA
> CAAGGGTGGGTCAGTAGGGGGTGTGCCCGCCAGGAGGGGTGGGTCTAAGGTGATAGAGCCTTCATTATAAATCT
> AGAGACTCCAGGATTTTAACGTTCTGCTGGACTGAGCTGGTTGCCTCATGTTATTATGCAGGCAACTCACTTTA
> TCCCAATTTCTTGATACTTTTCCTTCTGGAGGTCCTATTTCTCTAACATCTTCCAGAAAAGTCTTAAAGCTGCC
> TTAACCTTTTTTCCAGTCCACCTCTTAAATTTTTTCCTCCTCTTCCTCTATACTAACATGAGTGTGGATCCAGC
> TTGTCCCCAAAGCTTGCCTTGCTTTGAAGCATCCGACTGTAAAGAATCTTCACCTATGCCTGTGATTTGTGGGC
> CTGAAGAAAACTATCCATCCTTGCAAATGTCTTCTGCTGAGATGCCTCACACGGAGACTGGTAAGAAAGAAATT
> TATCCTTGAAAGGCCAAGTTCCTTAAGGGAAAAGAGAGAAGGAGAGAGGGTTAAGGGATCATTTCCCTCTTGAG
> CAATGATGGACCATTACTATAAAGAAGTGTTATTATCAACTAATCCTCTGGAAACCCCTTTTTCCATTATAACT
> TGGTGGCACCTGCCCTTTGAACTATGTCCCAGGTCTCAGGAGTGTGCATTGAGTTGAAGGACACAGAATTCGGC
> AGTTGAACAGTGTGCAGTAAGTTTGAGAACCTATGGGCTTAGGCATGGTGGAAACAAAAATGTATCGTTATAGT
> TAAATGAAGGTGATGTGTACATCTTCACATAGTGCTGGACACATGTGAATAAATAGCAGATTTATTGCTAATTA
> GCCA
> >
> GAAGACCTAACGTCATAGCTCAGGGATGAGCATGATTTTGTTTTGCCAAAAATGGCATGGCAAATCACGATGAG
> ATTTCTGTAATACATAATTTGGGTAATTCTTTCTATGTCAGTAACGGCTGTCTCTTCTCCATTCTCTGGGTTTG
> TGGATGTTACTGGGCAGCTCTGAGTTTGGGAGCACCTCCCATGTCTAATTCTCCTAAGTCCTGGGAAGCGTTGA
> CCCAACTTTATGGTAAAGATAATTCCAGAAAGTTTAATCTACTGACAGTCAAACAGAATGTAGCTAGAAGTCCA
> GTTTGGCTTCAAAACCTGTGCTAGTACTCATGCTTCTGACTGGTAGCTGCAAGGGGTGGGGGATACTCGGGATA
> CTCATAAAGCCGCTACCACTTTTTTGAAAATCAATTTTTCAGTAGTTTTCAAAAACTTGAGAATGAACCAACTT
> TACCAAGAATG',
> >                                            '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
> >> _______________________________________________
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> >> Bioperl-l at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/bioperl-l
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