Difference between revisions of "Blast"
| Line 9: | Line 9: | ||
'''An example blast''' | '''An example blast''' | ||
| − | blastall -p blastn -d /ibers/ | + | blastall -p blastn -d /ibers/repository/public/blast_db/latest/nt -i myfile.fasta -o myfile.blast -m 8 |
For some advice about running BLAST, take a look at [[[[Running BLAST optimally]]]] | For some advice about running BLAST, take a look at [[[[Running BLAST optimally]]]] | ||
| Line 17: | Line 17: | ||
The database directory is located; | The database directory is located; | ||
| − | /ibers/ | + | /ibers/repository/public/blast_db/ |
The following NCBI Databases are available; | The following NCBI Databases are available; | ||
| Line 24: | Line 24: | ||
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. | 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. | ||
| + | |||
| + | '''Legacy''' | ||
| + | |||
| + | Since the installation of the HPC, the blast databases have been stored in several location. As our storage capacity and needs changed, so did the location of the blast databases. Symbolic links exist in the old locations so that previous code, scripts and workflows continue to work. Here are the previous locations for reference. | ||
| + | |||
| + | /ibers/ernie/scratch/databases/ | ||
| + | /cm/shared/apps/BLAST/ncbi-blast-2.2.26+/db | ||
Revision as of 10:18, 9 July 2014
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/repository/public/blast_db/latest/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/repository/public/blast_db/
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.
Legacy
Since the installation of the HPC, the blast databases have been stored in several location. As our storage capacity and needs changed, so did the location of the blast databases. Symbolic links exist in the old locations so that previous code, scripts and workflows continue to work. Here are the previous locations for reference.
/ibers/ernie/scratch/databases/ /cm/shared/apps/BLAST/ncbi-blast-2.2.26+/db
