Difference between revisions of "Applications/Ncbi-blast"
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* windowmasker | * windowmasker | ||
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| + | ===Interactive Session=== | ||
| + | |||
| + | <pre style="background-color: #000; color: white; font-family: monospace, sans-serif;"> | ||
| + | |||
| + | [username@login01 ~]$ interactive | ||
| + | salloc: Granted job allocation 3619736 | ||
| + | Job ID 3619736 connecting to c081, please wait... | ||
| + | c081.vc-main | ||
| + | [username@c081 ~]$ module add ncbi-blast/2. | ||
| + | ncbi-blast/2.11.0 ncbi-blast/2.12.0 ncbi-blast/2.4.0 ncbi-blast/2.6.0 | ||
| + | [username@c081 ~]$ module add ncbi-blast/2.6.0 | ||
| + | [username@c081 ~] blastp <user options> | ||
| + | |||
| + | </pre> | ||
===Batch Script=== | ===Batch Script=== | ||
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module purge | module purge | ||
| − | module load ncbi-blast | + | module load ncbi-blast/2.6.0 |
blastp \ | blastp \ | ||
Latest revision as of 12:11, 17 November 2022
Contents
Application Details
- Description: NCBI-Blast finds regions of similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance.
- Version: 2.4.0 , 2.6.0
- Modules: ncbi-blast/2.4.0, ncbi-blast/2.6.0
- Licence: Open-source (BLAST is a registered trademark of the National Library of Medicine)
Usage Examples
Command Set
ncbi-blast provides the following commands:
- blast_formatter
- blastdb_aliastool
- blastdbcheck
- blastdbcmd
- blastn
- blastp
- blastx
- convert2blastmask
- deltablast
- dustmasker
- legacy_blast.pl
- makeblastdb
- makembindex
- makeprofiledb
- psiblast
- rpsblast
- rpstblastn
- segmasker
- tblastn
- tblastx
- update_blastdb.pl
- windowmasker
Interactive Session
[username@login01 ~]$ interactive salloc: Granted job allocation 3619736 Job ID 3619736 connecting to c081, please wait... c081.vc-main [username@c081 ~]$ module add ncbi-blast/2. ncbi-blast/2.11.0 ncbi-blast/2.12.0 ncbi-blast/2.4.0 ncbi-blast/2.6.0 [username@c081 ~]$ module add ncbi-blast/2.6.0 [username@c081 ~] blastp <user options>
Batch Script
#!/bin/bash
#SBATCH -J blast
#SBATCH -N 1
#SBATCH --ntasks-per-node 1
#SBATCH -o job-%j.out
#SBATCH -e job-%j.out
#SBATCH -p compute
# perfoms NR blast (blastx)
infile="$1"
outfile="$(basename "${infile%.*}").xml"
database="/swissprot/uniprot_sprot"
module purge
module load ncbi-blast/2.6.0
blastp \
-query "${infile}" \
-db "${database}" \
-out "${outfile}".xml \
-evalue 1e-5 \
-num_threads 8 \
-max_target_seqs 50 \
-outfmt 5