BLAST+-Teaching
Category
Bioinformatics
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 loads 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 at 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
Installation
Source code is obtained from BLAST+
System
64-bit Linux