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Old 08-23-2011, 02:54 AM   #1
Sheera
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Location: Galway

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Default Naive issue of database download

Hello All,

I am trying to download the whole genome(nt) sequences for different species. But I don't get any single file for that.
Eg I go to

NCBI RefSeq FTP-> Genomes-> Homo sapiens
ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/

The sequences are spread over different chromosomes.
Should I download each chromosome and concatenate into one file or there is some other option?

thanks,
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Old 08-23-2011, 05:05 AM   #2
sdvie
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Sheera, concatenating is one option.

Depending on the species that you need, you might also find what you are looking for here:
http://hgdownload.cse.ucsc.edu/downloads.html

cheers!
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Old 08-24-2011, 03:59 AM   #3
Sheera
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Thanks for the reply.
But this concatenated dataset would serve as an database for the local stand alone blast+.

I have to download almost all mammalian.
Any better way of downloading the genomes.
Thanks.
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Old 08-24-2011, 04:37 AM   #4
GenoMax
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Have you considered downloading pre-built blast index files from NCBI: ftp://ftp.ncbi.nlm.nih.gov/blast/db/
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Old 08-24-2011, 09:37 AM   #5
Sheera
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Thanks GenoMax!
But I am not agree I am not at itagain.
I downloaded refseq_genomic_tar.gz data file from ftp://ftp.ncbi.nlm.nih.gov/blast/db/ like this

./update_blastdb.pl ftp://ftp.ncbi.nlm.nih.gov/blast/db/ refseq_genomic*

I gunzip and got like 8 files as:
refseq_genomic.nhr
refseq_genomic.nin
refseq_genomic.nid
refseq_genomic.nnd
refseq_genomic.nog
refseq_genomic.nsi n more.
I want to make this as file as my local database for the further blast thing.
I have new blast ie blast+ working

Now for formatdb, its makeblastdb.

I dont know how the downloaded file works here as I tried many ways.
./makeblastdb -i refseq_genomic.tar.gz -title ref_data -out ref_data


Someone any idea how it should be proceeded?
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Old 08-24-2011, 10:50 AM   #6
GenoMax
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These are pre-made blast index files. You can start using them right away after extracting them from the archive.


Quote:
Originally Posted by Sheera View Post
Thanks GenoMax!
But I am not agree I am not at itagain.
I downloaded refseq_genomic_tar.gz data file from ftp://ftp.ncbi.nlm.nih.gov/blast/db/ like this

./update_blastdb.pl ftp://ftp.ncbi.nlm.nih.gov/blast/db/ refseq_genomic*

I gunzip and got like 8 files as:
refseq_genomic.nhr
refseq_genomic.nin
refseq_genomic.nid
refseq_genomic.nnd
refseq_genomic.nog
refseq_genomic.nsi n more.
I want to make this as file as my local database for the further blast thing.
I have new blast ie blast+ working

Now for formatdb, its makeblastdb.

I dont know how the downloaded file works here as I tried many ways.
./makeblastdb -i refseq_genomic.tar.gz -title ref_data -out ref_data


Someone any idea how it should be proceeded?
GenoMax is offline   Reply With Quote
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