BLAST+-Teaching: Difference between revisions

Revision as of 13:41, 10 August 2018

Program On

Teaching

Version

2.6.0

Author / Distributor

Description

"Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences." More details are at BLAST+

Running Program

The last version of this application is at /usr/local/apps/eb/BLAST+/2.6.0-foss-2016b-Python-2.7.14

To use this version, please load the module with

ml BLAST+/2.6.0-foss-2016b-Python-2.7.14

Here is an example of a shell script, sub.sh, to run on the batch queue:

#!/bin/bash
#SBATCH --job-name=j_BLAST+
#SBATCH --partition=batch
#SBATCH --mail-type=ALL
#SBATCH --mail-user=username@uga.edu
#SBATCH --ntasks=1
#SBATCH --mem=10gb
#SBATCH --time=08:00:00
#SBATCH --output=BLAST+.%j.out

cd $SLURM_SUBMIT_DIR
ml BLAST+/2.6.0-foss-2016b-Python-2.7.14
blastn [options]

In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values.

Please refer to Running_Jobs_on_the_teaching_cluster, Run X window Jobs and Run interactive Jobs for more details of running jobs at Teaching cluster.

Here is an example of job submission command:

sbatch ./sub.sh

Documentation

ml BLAST+/2.6.0-foss-2016b-Python-2.7.14 
blastn blastn -h
USAGE
  blastn [-h] [-help] [-import_search_strategy filename]
    [-export_search_strategy filename] [-task task_name] [-db database_name]
    [-dbsize num_letters] [-gilist filename] [-seqidlist filename]
    [-negative_gilist filename] [-entrez_query entrez_query]
    [-db_soft_mask filtering_algorithm] [-db_hard_mask filtering_algorithm]
    [-subject subject_input_file] [-subject_loc range] [-query input_file]
    [-out output_file] [-evalue evalue] [-word_size int_value]
    [-gapopen open_penalty] [-gapextend extend_penalty]
    [-perc_identity float_value] [-qcov_hsp_perc float_value]
    [-max_hsps int_value] [-xdrop_ungap float_value] [-xdrop_gap float_value]
    [-xdrop_gap_final float_value] [-searchsp int_value]
    [-sum_stats bool_value] [-penalty penalty] [-reward reward] [-no_greedy]
    [-min_raw_gapped_score int_value] [-template_type type]
    [-template_length int_value] [-dust DUST_options]
    [-filtering_db filtering_database]
    [-window_masker_taxid window_masker_taxid]
    [-window_masker_db window_masker_db] [-soft_masking soft_masking]
    [-ungapped] [-culling_limit int_value] [-best_hit_overhang float_value]
    [-best_hit_score_edge float_value] [-window_size int_value]
    [-off_diagonal_range int_value] [-use_index boolean] [-index_name string]
    [-lcase_masking] [-query_loc range] [-strand strand] [-parse_deflines]
    [-outfmt format] [-show_gis] [-num_descriptions int_value]
    [-num_alignments int_value] [-line_length line_length] [-html]
    [-max_target_seqs num_sequences] [-num_threads int_value] [-remote]
    [-version]

DESCRIPTION
   Nucleotide-Nucleotide BLAST 2.6.0+

Use '-help' to print detailed descriptions of command line arguments

Back to Top

Installation

Source code is obtained from BLAST+

System

64-bit Linux

@@ Line 23: / Line 23: @@
 The last version of this application is at /usr/local/apps/eb/BLAST+/2.6.0-foss-2016b-Python-2.7.14
-To use this version, please loads the module with
+To use this version, please load the module with
 <pre class="gscript">
 ml BLAST+/2.6.0-foss-2016b-Python-2.7.14
 </pre>
-Here is an example of a shell script, sub.sh, to run on at the batch queue:
+Here is an example of a shell script, sub.sh, to run on the batch queue:
 <div class="gscript2">
 <nowiki>#</nowiki>!/bin/bash<br>
-<nowiki>#</nowiki>SBATCH --job-name=BLAST+<br>
+<nowiki>#</nowiki>SBATCH --job-name=j_BLAST+<br>
 <nowiki>#</nowiki>SBATCH --partition=batch<br>
 <nowiki>#</nowiki>SBATCH --mail-type=ALL<br>