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Old 03-02-2011, 05:46 AM   #1
andreitudor
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Question Blast+ database with gene annotation

Hello,

I have been trying for the last few days to make a blast database (with blast+ tools) that would contain the gene information from a genebank file. Is it possible to do that with blast+ or with bioperl?
I have been looking at bioperl and it looks like you can add the annotation information to a sequence object, but I don't relly understand which object should I use. There is not a lot of information on this, not even in the bioperl docs.

Thanks,
Andrei
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Old 03-02-2011, 02:04 PM   #2
kmcarr
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Andrei,

BLAST databases aren't designed to contain a large amount of annotation about a sequence, and you can't create one directly from a GenBank file. The input to makeblastdb must be a FASTA formatted file (or an existing BLASTDB you want to alter). The text on the definition (description) line for each sequence is stored in the BLASTdb but just as a plain text string.

The more reasonable approach would be to read the accession or gi numbers from the BLAST hits and then use those to query GenBank or a local database for annotation.
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Old 03-03-2011, 06:57 AM   #3
andreitudor
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OK, so blast+ does not do this automatically. Then I should be able to do this with bioperl. There should be an object that can get the genbank information from a file and then you could compare it to a SeqIO object that contains the corresponding sequence.

What I want to do is compare a query sequence to a blast database and see which gene from that database corresponds to that query. Also print out the parcentage of the matching nucleotides.

In order to do this I think I must first get the sequence for each gene that is found in the genebank file from the blast database. Then BLAST my query sequence against the gene sequences and get the one that matches the best.

Does this make any sense to anyone else?

Andrei
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Old 03-03-2011, 07:07 AM   #4
colindaven
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Why not follow kmcarr's suggestion - first Blast, then lookup the accessions in a annotation file or db?

That's how I'd do it too.
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Old 03-03-2011, 07:26 AM   #5
andreitudor
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And how do I do that? The computer that I am working from has no internet connection, so I have to download all the genbank files that contain the gene information. I can make a local database from them too, as you can make with the fasta sequences?

Last edited by andreitudor; 03-03-2011 at 07:32 AM.
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