Bureaucrats, cc_docs_admin, cc_staff
2,879
edits
BLAST: Difference between revisions
Jump to navigation
Jump to search
Marked this version for translation
(link to Genomics data) |
(Marked this version for translation) |
||
| Line 3: | Line 3: | ||
<translate> | <translate> | ||
<!--T:1--> | |||
BLAST ("Basic Local Alignment Search Tool") finds regions of similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance. | BLAST ("Basic Local Alignment Search Tool") finds regions of similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance. | ||
<!--T:2--> | |||
BLAST searches can be run over the Internet using the [https://blast.ncbi.nlm.nih.gov/Blast.cgi NCBI site], but you '''should not do this''' for production work on a Compute Canada cluster. Instead load the BLAST+ [[Utiliser des modules/en|module]] and a search database on the cluster. | BLAST searches can be run over the Internet using the [https://blast.ncbi.nlm.nih.gov/Blast.cgi NCBI site], but you '''should not do this''' for production work on a Compute Canada cluster. Instead load the BLAST+ [[Utiliser des modules/en|module]] and a search database on the cluster. | ||
<!--T:3--> | |||
Some frequently-used sequence databases are installed on Compute Canada clusters. See [[Genomics data]]. | Some frequently-used sequence databases are installed on Compute Canada clusters. See [[Genomics data]]. | ||
== Performance == | == Performance == <!--T:4--> | ||
<!--T:5--> | |||
Here are some things to try in order to accelerate your BLAST search on a computer cluster: | Here are some things to try in order to accelerate your BLAST search on a computer cluster: | ||
<!--T:6--> | |||
* Copy your FASTA database to node-local storage (<code>$SLURM_TMPDIR</code>) and run <code>makeblastdb</code> at beginning of your job script to generate your blast db on ramdisk on the node. | * Copy your FASTA database to node-local storage (<code>$SLURM_TMPDIR</code>) and run <code>makeblastdb</code> at beginning of your job script to generate your blast db on ramdisk on the node. | ||
* Use multi-threading (option <code>-num_threads</code>). Beware that this is not very efficient; test to determine a suitable number of threads. | * Use multi-threading (option <code>-num_threads</code>). Beware that this is not very efficient; test to determine a suitable number of threads. | ||