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Which BLAST db to download for mouse genome?


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#1 A.N.Other

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Posted 19 May 2011 - 07:53 AM

I've got local BLAST+ set up on a few computers here and I've been using it for a while against my own compiled databases. However I'd now also like to do some BLASTing against the mouse genome - something I've always done online in the past.

For the life of me I can't work out from the BLAST documentation which files I actually need to download from their FTP server to achieve this. Can someone point me in the right direction? I'm after the file/s for the mouse genomic reference assembly - I don't need transcripts, or anything other than that (unless they're all bundled together anyway).

From the server I can see the refseq_genomic_**.tar.gz files but that doesn't specify species, so I assume that includes the human assemblies as well. Given that there are 35 of them at 1Gb a piece, I'm hoping there's somewhere I can get the files for only the mouse sequence?

Thanks in advance :)

Edited by A.N.Other, 19 May 2011 - 08:00 AM.


#2 CHODAR

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Posted 19 May 2011 - 03:17 PM

I've got local BLAST+ set up on a few computers here and I've been using it for a while against my own compiled databases. However I'd now also like to do some BLASTing against the mouse genome - something I've always done online in the past.

For the life of me I can't work out from the BLAST documentation which files I actually need to download from their FTP server to achieve this. Can someone point me in the right direction? I'm after the file/s for the mouse genomic reference assembly - I don't need transcripts, or anything other than that (unless they're all bundled together anyway).

From the server I can see the refseq_genomic_**.tar.gz files but that doesn't specify species, so I assume that includes the human assemblies as well. Given that there are 35 of them at 1Gb a piece, I'm hoping there's somewhere I can get the files for only the mouse sequence?

Thanks in advance :)


The ResSeq multi-species database and contains curated sequences from NCBI, so it's a huge database. Take a look to this page:
NCBI RefSeq Project.

Maybe you can try download the mouse sequences from ENSEMBL databases and convert with formatdb command. Here's the link to sequences.
ENSEMBL FTP

Good luck.

Christian.

Edited by CHODAR, 19 May 2011 - 03:22 PM.


#3 A.N.Other

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Posted 20 May 2011 - 02:53 AM

Thanks. I downloaded the files from ENSEMBL and compiled them with makeblastdb and blastdb_aliastool.

All sorted and up and running. Thanks for the quick response :)




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