[Bioperl-l] Re: problem in /usr/lib/perl5/site_perl/5.8.6/Bio/SearchIO/blast.pm

[Jason Stajich]

This is from RemoteBlast or from blast run on the command line?

On Jan 13, 2006, at 5:47 AM, Guido Dieterich wrote:

> Hi Jason, hi all,
>
> it seems  so that ncbi changed again its blast output format:
> as example:
> they added a/more Feature line(s)
>>>>>
> Features in this part of subject sequence:
>    oxidoreductase, pyridine nucleotide-disulfide family
>>>>>
>
>
> Bio/SearchIO/blast.pm
>
> will cause a problem. Error message is:
>
> ------------- EXCEPTION: Bio::Root::Exception -------------
> MSG: no data for midline  Features flanking this part of subject
> sequence:
> STACK: Error::throw
> STACK:
> Bio::Root::Root::throw /usr/lib/perl5/site_perl/5.8.6/Bio/Root/ 
> Root.pm:328
> STACK:
> Bio::SearchIO::blast::next_result /usr/lib/perl5/site_perl/5.8.6/ 
> Bio/SearchIO/blast.pm:1166
> STACK: main::remoteBLAST /home/gdi/Perl-skripte/longestORF.pl:95
> STACK: /home/gdi/Perl-skripte/longestORF.pl:34
> -----------------------------------------------------------
>
>
>
> longer example of the blast ncbi report:
>
>> gb|AE016830.1| Enterococcus faecalis V583, complete genome
>           Length=3218031
>
>  Features in this part of subject sequence:
>    oxidoreductase, pyridine nucleotide-disulfide family
>
>  Score = 79.8 bits (40),  Expect = 3e-11
>  Identities = 82/96 (85%), Gaps = 0/96 (0%)
>  Strand=Plus/Plus
>
> Query  1129
> ATGAAACATATGGTTAACTTGTACTACTTCTTCGGTATCCGTAGTGGTTACTACATGTGG  1188
>                 ||||||||||| ||||||||| | |||||||| | ||| |||
> ||||||||||||||
> Sbjct  3136253
> ATGAAACATATCGTTAACTTGAAATACTTCTTTGATATTCGTTCTGGTTACTACATGTTC  3136312
>
> Query  1189     CAATATATTATGCATGAATTCTTCCACATTAAAGAT  1224
>                 ||||| |||||||| ||| ||||||| |||||||||
> Sbjct  3136313  CAATACATTATGCACGAAATCTTCCATATTAAAGAT  3136348
>
>
>  Features in this part of subject sequence:oxidoreductase, pyridine
> nucleotide-disulfide family
>
>  Score = 77.8 bits (39),  Expect = 1e-10
>  Identities = 90/107 (84%), Gaps = 0/107 (0%)
>  Strand=Plus/Plus
>
> Query  469
> AAAGCGATGTTAACATTCGTTGTTTGTGGATCTGGATTTACTGGTATCGAAATGGTTGGG  528
>                 ||||| ||||||||||||||||| ||||| ||||| ||||||||  
> |||||||||||
> ||
> Sbjct  3135587
> AAAGCAATGTTAACATTCGTTGTCTGTGGTTCTGGTTTTACTGGGATCGAAATGGTCGGC  3135646
>
> Query  529      GAACTTTTAGAATGGAAAGATCGTCTTGCTAAAGATAACAAAATTGA  575
>                 ||| |  | || |||||||||||| | || ||||||  |||||||||
> Sbjct  3135647  GAATTAATCGACTGGAAAGATCGTTTAGCGAAAGATGCCAAAATTGA   
> 3135693
>
>

--
Jason Stajich
jason at bioperl.org
http://jason.open-bio.org/