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 | ||
| + | |||
| + | There are additional versions of blast available. Check using the module avail command in the [[Module Environment]]. | ||
'''An example blast''' | '''An example blast''' | ||
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/ibers/repository/public/blast_db/ | /ibers/repository/public/blast_db/ | ||
| + | |||
| + | You will see something like the following; | ||
| + | |||
| + | [user@bert blast_db]# ls | ||
| + | blast_july blast_june blast_may latest | ||
| + | |||
| + | '''Notes about using NCBI Databases''' | ||
| + | |||
| + | 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. | ||
| + | |||
| + | You will find that in this directory there are the last three months of blast databases in separate directories, along with a symbolic link to the latest. This is because it is not possible to update a blast database while it is in use. If a blast run is quick, and not near the 1st of the month, then simply using the latest blast directory is fine. However, if you wish to be cautious or think that your blast run is going to take a while, then use the databases from the most recent month. | ||
The following NCBI Databases are available; | The following NCBI Databases are available; | ||
16SMicrobial env_nt nt refseq_protein refseq_rna nr | 16SMicrobial env_nt nt refseq_protein refseq_rna nr | ||
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| − | |||
'''Legacy''' | '''Legacy''' | ||
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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. | 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/ | + | /ibers/ernie/scratch/databases/ |
| − | /cm/shared/apps/BLAST/ncbi-blast-2.2.26+/db | + | |
| + | /cm/shared/apps/BLAST/ncbi-blast-2.2.26+/db | ||
Latest revision as of 10:36, 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
There are additional versions of blast available. Check using the module avail command in the Module Environment.
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/
You will see something like the following;
[user@bert blast_db]# ls blast_july blast_june blast_may latest
Notes about using NCBI Databases
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.
You will find that in this directory there are the last three months of blast databases in separate directories, along with a symbolic link to the latest. This is because it is not possible to update a blast database while it is in use. If a blast run is quick, and not near the 1st of the month, then simply using the latest blast directory is fine. However, if you wish to be cautious or think that your blast run is going to take a while, then use the databases from the most recent month.
The following NCBI Databases are available;
16SMicrobial env_nt nt refseq_protein refseq_rna nr
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
