Difference between revisions of "Running BLAST optimally"
(Created page with "This is a brief description of a couple of experiments that I (mjv08) have tried out using blast in order to determine the best way in which to run it. Okay, so you have a fa...") |
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| − | This is a brief description of a couple of experiments that I (mjv08) have tried out using blast in order to determine the best way in which to run it. | + | This is a brief description of a couple of experiments that I (mjv08) have tried out using blast in order to determine the best way in which to run it. |
Okay, so you have a fasta file you wish to blast. The file I had was supplied by Russ (rom) and contained 18788 sequences in a fasta file. He wanted to run the default settings for blast using blast2go. These settings using blast+ on the command line are; | Okay, so you have a fasta file you wish to blast. The file I had was supplied by Russ (rom) and contained 18788 sequences in a fasta file. He wanted to run the default settings for blast using blast2go. These settings using blast+ on the command line are; | ||
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blastx -db nr -query input.fasta -out output.xml -evalue 1e-3 -outfmt 5 -show_gis -num_threads 1 | blastx -db nr -query input.fasta -out output.xml -evalue 1e-3 -outfmt 5 -show_gis -num_threads 1 | ||
| − | + | The first thing I have done is to take a single sequence, | |
| − | + | [[File:Example.jpg]] | |
Revision as of 14:14, 7 August 2013
This is a brief description of a couple of experiments that I (mjv08) have tried out using blast in order to determine the best way in which to run it.
Okay, so you have a fasta file you wish to blast. The file I had was supplied by Russ (rom) and contained 18788 sequences in a fasta file. He wanted to run the default settings for blast using blast2go. These settings using blast+ on the command line are;
blastx -db nr -query input.fasta -out output.xml -evalue 1e-3 -outfmt 5 -show_gis -num_threads 1
The first thing I have done is to take a single sequence,
