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01-02-2010, 12:14 AM
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#1 |
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Member
Location: Singapore Join Date: Nov 2009
Posts: 14
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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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01-04-2010, 07:23 AM
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#2 |
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Senior Member
Location: Boston area Join Date: Nov 2007
Posts: 747
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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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