Difference between revisions of "Blast"
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blastall blastclust blastdb_aliastool blastdbcheck blastdbcmd blast_formatter blastn blastp blastpgp blastx | blastall blastclust blastdb_aliastool blastdbcheck blastdbcmd blast_formatter blastn blastp blastpgp blastx | ||
| − | + | '''An example blast''' | |
| + | |||
| + | blastall -p blastn -d /ibers/ernie/scratch/databases/blast/nt -i myfile.fasta -o myfile.blast -m 8 | ||
| − | + | For some advice about running BLAST, take a look at [[[[Running BLAST optimally]]]] | |
| − | + | '''NCBI Databases''' | |
The database directory is located; | The database directory is located; | ||
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/ibers/ernie/scratch/databases/blast | /ibers/ernie/scratch/databases/blast | ||
| − | + | The following NCBI Databases are available; | |
| − | |||
| − | |||
| − | + | 16SMicrobial env_nt nt refseq_protein refseq_rna nr | |
| − | + | These are updated at midnight on the first day of the month. It is advisable NOT to be running a blast using these databases on at midnight on the first day of the month. It is possible that something odd things may happen if a database is updated while the job is running. | |
Revision as of 15:46, 30 October 2013
BLAST can be loaded using the following command;
[user@ernie ]# module load BLAST/blast-2.2.26
This loads both blast-2.2.26 and ncbi-blast-2.2.26+, giving you access to commands such as;
blastall blastclust blastdb_aliastool blastdbcheck blastdbcmd blast_formatter blastn blastp blastpgp blastx
An example blast
blastall -p blastn -d /ibers/ernie/scratch/databases/blast/nt -i myfile.fasta -o myfile.blast -m 8
For some advice about running BLAST, take a look at [[Running BLAST optimally]]
NCBI Databases
The database directory is located;
/ibers/ernie/scratch/databases/blast
The following NCBI Databases are available;
16SMicrobial env_nt nt refseq_protein refseq_rna nr
These are updated at midnight on the first day of the month. It is advisable NOT to be running a blast using these databases on at midnight on the first day of the month. It is possible that something odd things may happen if a database is updated while the job is running.
