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Old 04-07-2011, 11:44 PM   #1
rururara
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Location: montreal

Join Date: Jan 2011
Posts: 31
Default convert blast output

hai all,

do you know how to convert blastall output into txt or gff format?

eg:

Query= OsSNP0002
(142 letters)

Database: ../u01/perl/uniprot-oryza-sativa-indica.fasta
42,240 sequences; 15,872,719 total letters

Searching..................................................done



Score E
Sequences producing significant alignments: (bits) Value

tr|A2WJN5|A2WJN5_ORYSI Putative uncharacterized protein OS=Oryza... 55 2e-18
tr|B8AKP7|B8AKP7_ORYSI Putative uncharacterized protein OS=Oryza... 53 6e-17
tr|B8AEL6|B8AEL6_ORYSI Putative uncharacterized protein OS=Oryza... 28 1.5
tr|B8B114|B8B114_ORYSI Putative uncharacterized protein OS=Oryza... 28 2.0
tr|B8AQS5|B8AQS5_ORYSI Putative uncharacterized protein OS=Oryza... 27 2.6
tr|B8ADP7|B8ADP7_ORYSI Putative uncharacterized protein OS=Oryza... 27 4.4
tr|A2ZKU4|A2ZKU4_ORYSI Putative uncharacterized protein OS=Oryza... 26 7.5
tr|A2Y774|A2Y774_ORYSI Putative uncharacterized protein OS=Oryza... 26 7.5
tr|A2WXP8|A2WXP8_ORYSI Putative uncharacterized protein OS=Or
yza... 25 9.7

thanks!
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Old 04-08-2011, 01:48 AM   #2
Thorondor
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Location: Heidelberg

Join Date: Feb 2011
Posts: 69
Default

this is in text format, so you don't need to format it. ;-)

to get it into gff, look at:

http://biostar.stackexchange.com/que...results-to-gff
http://www.bioperl.org/wiki/HOWTO:Gr...l_BLAST_Output

actually it is not totally clear to me what you want and sometimes it is worth the time to ask a search engine first.
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