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Old 01-02-2010, 12:14 AM   #1
CarlElit
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Location: Singapore

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Default Database of BLAST

Hello, everyone.

Now I am doing alignment using BLAST. I want to align some sequences (FASTA format) against human chromosome. I used HG18 from UCSC (<http://hgdownload.cse.ucsc.edu/goldenPath/hg18/chromosomes/>) before with Bowtie. Are there pre-processed db on the FTP of BLAST (ftp://ftp.ncbi.nlm.nih.gov/blast/db/), which is built from HG18? I am a freshman to Bio...

Thanks a lot.
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Old 01-04-2010, 07:23 AM   #2
krobison
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The BLAST binaries contain the formatdb utility which is all you need to generate the indices prior to running BLAST

formatdb -p F -d hg18.fa

Would index the nucleotide file (-p F specifies that this is (F)alse for (p)rotein) named hg81.fa
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