Overview
BLAST: In bioinformatics, BLAST is an algorithm and program for comparing primary biological sequence information, such as the amino-acid sequences of proteins or the nucleotides of DNA and/or RNA sequences.
Using
Use the module name blast-plus to discover versions available and to load the application.
Example
[]$ 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 and WilidIirs 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.
Here is a list of the current databases on Teton:
Teton | WildIris |
|---|---|
Last updated: 20210422 | Last updated: 20220312 |
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 cdd_delta env_nr env_nt human_genome landmark mito mouse_genome nr nt pataa patnt pdbaa pdbnt ref_euk_rep_genomes ref_prok_rep_genomes ref_viroids_rep_genomes ref_viruses_rep_genomes refseq_protein refseq_rna refseq_select_prot refseq_select_rna swissprot taxdb tsa_nr tsa_nt | 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 env_nt env_nr human_genome landmark mito mouse_genome nr nt pataa patnt pdbaa pdbnt ref_euk_rep_genomes ref_prok_rep_genomes ref_viroids_rep_genomes ref_viruses_rep_genomes refseq_select_rna refseq_select_prot refseq_protein refseq_rna swissprot tsa_nr tsa_nt 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.