[Bioperl-l] How to extract organism information from blast report?

[ying lin]

I thought that as methods to extract name and description as well as a
bunch of other hit information have been provided, there should be some
method to extract hit organism.

Below is one example of hsp which has the [ORGANISM] information after
name and description excerpted from blast report:

>gi|3348131|gb|AAC27796.1|   cytoplasmic beta actin [Xenopus laevis]
 gi|27735427|gb|AAH41203.1|   similar to actin, beta, cytoplasmic [Xenopus
laevis]
          Length = 375

 Score =  754 bits (1947), Expect = 0.0
 Identities = 371/375 (98%), Positives = 375/375 (100%)
 Frame = +2

Query: 89   MEEEIAALVIDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQS
268
            ME++IAALV+DNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQS
Sbjct: 1    MEDDIAALVVDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQS
60

Query: 269  KRGILTLKYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKMT
448
            KRGILTLKYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKMT
Sbjct: 61   KRGILTLKYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKMT
120

Query: 449  QIMFETFNTPAMYVAIQAVLSLYASGRTTGIVMDSGDGVTHTVPIYEGYALPHAILRLDL
628
            QIMFETFNTPAMYVAIQAVLSLYASGRTTGIVMDSGDGVTHTVPIYEGYALPHAILRLDL
Sbjct: 121  QIMFETFNTPAMYVAIQAVLSLYASGRTTGIVMDSGDGVTHTVPIYEGYALPHAILRLDL
180

Query: 629  AGRDLTDYLMKILTERGYSFTTTAEREIVRDIKEKLCYVALDFEQEMATAASSSSLEKSY
808
            AGRDLTDYLMKILTERGYSFTTTAEREIVRDIKEKLCYVALDFEQEMATAASSSSLEKSY
Sbjct: 181  AGRDLTDYLMKILTERGYSFTTTAEREIVRDIKEKLCYVALDFEQEMATAASSSSLEKSY
240

Query: 809  ELPDGQVITIGNERFRCPEALFQPSFLGMESCGIHETTFNSIMKCDVDIRKDLYANTVLS
988
            ELPDGQVITIGNERFRCPEALFQPSFLGMESCGIHETT+NSIMKCDVDIRKDLYANTVLS
Sbjct: 241  ELPDGQVITIGNERFRCPEALFQPSFLGMESCGIHETTYNSIMKCDVDIRKDLYANTVLS
300

Query: 989  GGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWISKQ
1168
            GGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWISKQ
Sbjct: 301  GGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWISKQ
360

Query: 1169 EYDESGPSIVHRKCF 1213
            EYDESGPSIVHRKCF
Sbjct: 361  EYDESGPSIVHRKCF 375





Ying Lin
Dept. of Computer and Information Sciences
University of Delaware

On Tue, 1 Jul 2003, Jason Stajich wrote:

> Is the organism's name actually in the report?
>
> With SearchIO,
> $hit->name, $hit->description will give you whatever is in the report.
>
> -jason
> On Tue, 1 Jul 2003, ying lin wrote:
>
> > Hi,I have been trying to find the method to extract the organism's name of
> > hits in blast report but can't find it.Can anyone tell me what is
> > that?Thanks!
> >
> > Ying Lin
> > Dept. of Computer and Information Sciences
> > University of Delaware
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at portal.open-bio.org
> > http://portal.open-bio.org/mailman/listinfo/bioperl-l
> >
>
> --
> Jason Stajich
> Duke University
> jason at cgt.mc.duke.edu
>