[Bioperl-l] How to extract organism information from blast report?
ying lin
ylin at mail.eecis.udel.edu
Tue Jul 1 13:12:26 EDT 2003
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
>
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