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Old 10-04-2010, 02:47 AM   #1
NicoBxl
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Location: Belgium

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Default blast database creation ( multiple file )

Hi,

I'm a newbie in standalone blast. I'm working on the Bos Taurus Genome. My question is how to make a blast database of the bos taurus genome. On the NCBI ftp site in the bos taurus genome directory ( ftp://ftp.ncbi.nih.gov/genomes/Bos_taurus/ ) there's a lot of file . Which on is the good one to create this database. Other question, how to combine chromosomes files to create one database ?

Thanks a lot,

Nicolas
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Old 10-04-2010, 11:04 AM   #2
westerman
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There are lots of files since the Bos Taurus genome is far from complete. People have various ways that they want to deal with the incomplete data.

Since I am not in your shoes I can not say for certain, but I suspect that taking the 'bt_ref*.fa' (non-masked reference chromosomsal) files from the assembled section ( ftp://ftp.ncbi.nih.gov/genomes/Bos_t...romosomes/seq/ ) will be want you want to do. As for combining the files, the blast database creation program (aka, 'formatdb') will do this for you if you put multiple files after the '-i' option.
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Old 10-05-2010, 12:19 AM   #3
NicoBxl
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ok thanks, I'll try that

Do I take the bt_ref_*_unplaced.fa ?

on the ncbi blast site, when a blast serach on bos taurus genome is done, which sequence is taken ?

Last edited by NicoBxl; 10-05-2010 at 12:37 AM.
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Old 10-05-2010, 02:40 AM   #4
francois.sabot
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Either, put all the files in the same folder, and then launch the following command:

Quote:
cat *.fa > complete_bos.fasta && formatdb -i complete_bos.fasta -p F
All your fasta files will be written in complete_bos.fasta and the formatting will be performed after.

This command will work on Unix-like only, not in WinM$
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