Difference between revisions of "BLAST"

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Revision as of 23:33, 25 March 2020

  • Homepage: BLAST:
    • Manual:
    • Blast database last updated: 20200325


Module: Example

[]$ module spider blast-plus
----------------------------------------------
  blast-plus:
----------------------------------------------
     Versions:
        blast-plus/2.6.0-py27
        blast-plus/2.10.0-py27
----------------------------------------------
  For detailed information about a specific "blast-plus" module (including how to load the modules) use the module's full name.
  For example:

     $ module spider blast-plus/2.6.0-py27
----------------------------------------------
[]$ module load gcc/7.3.0
[]$ module load blast-plus/2.10.0-py27

[]$ blastp -help
USAGE
  blastp [-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] [-negative_seqidlist filename]
    [-taxids taxids] [-negative_taxids taxids] [-taxidlist filename]
    [-negative_taxidlist filename] [-ipglist filename]
    [-negative_ipglist 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]
    [-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] [-seg SEG_options]
    [-soft_masking soft_masking] [-matrix matrix_name]
    [-threshold float_value] [-culling_limit int_value]
    [-best_hit_overhang float_value] [-best_hit_score_edge float_value]
    [-subject_besthit] [-window_size int_value] [-lcase_masking]
    [-query_loc range] [-parse_deflines] [-outfmt format] [-show_gis]
    [-num_descriptions int_value] [-num_alignments int_value]
    [-line_length line_length] [-html] [-sorthits sort_hits]
    [-sorthsps sort_hsps] [-max_target_seqs num_sequences]
    [-num_threads int_value] [-ungapped] [-remote] [-comp_based_stats compo]
    [-use_sw_tback] [-version]

DESCRIPTION
   Protein-Protein BLAST 2.10.0+

OPTIONAL ARGUMENTS
 -h
   Print USAGE and DESCRIPTION;  ignore all other parameters
 -help
   Print USAGE, DESCRIPTION and ARGUMENTS; ignore all other parameters
 -version
   Print version number;  ignore other arguments
...

Blast Database

ARCC has a version of the related BLAST database installed on teton that is configured so that blast knows where to look for it (so you don't have to worry about this).
Due to the reasonably dynamic nature of this database, ARCC does have a method to update this database on request.
As of 20200325, here is a list of the current databases:

Connected to NCBI
16S_ribosomal_RNA
18S_fungal_sequences
28S_fungal_sequences
Betacoronavirus
ITS_RefSeq_Fungi
ITS_eukaryote_sequences
LSU_eukaryote_rRNA
LSU_prokaryote_rRNA
SSU_eukaryote_rRNA
landmark
nr
nt
patnt
pdbaa
pdbnt
ref_euk_rep_genomes
ref_prok_rep_genomes
ref_viroids_rep_genomes
ref_viruses_rep_genomes
refseq_protein
refseq_rna
swissprot
taxdb

Version: 2.6.10

Since the last update of the database, version 2.6.0 is no longer compatible with this database. If you try running blastp with this version, you will see the following error message:

BLAST Database error: Error: Not a valid version 4 database.

Using:

Basic Batch Script

#!/bin/bash
#SBATCH --job-name blastp
#SBATCH --nodes=1
#SBATCH --cpus-per-task=16
#SBATCH --time=24:00:00
#SBATCH --account=<your account>

module load swset/2018.05 gcc/7.3.0
module load blast-plus/2.10.0-py27

srun blastp <add input files and configuration>

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