BlastX on command line

Question

[marongiu.luigi]

Dear all,

is it possible to run BlastX on the command line? I have installed Nucleotide-Nucleotide BLAST 2.5.0+; what would be the syntax (if I can use this program) or when can I find blastX? Thank you

Answer 1

[Joe]

This is where you should start: https://www.ncbi.nlm.nih.gov/books/NBK279690/

[marongiu.luigi]

OK, I think I found it: blastx is already included in the blast suite thus I only need to change the blast command with blastx

[Mark]

Yep you got it. The manual isn't that great unfortunately. But mostly all the options for blastn is similar for blastx.

[marongiu.luigi]

Among the tasks, I can see blastp, blastn and megablast but not blastX...

[Joe]

It's there:

$ blastx -help
USAGE
  blastx [-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]
    [-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] [-max_intron_length length] [-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]
    [-window_size int_value] [-ungapped] [-lcase_masking] [-query_loc range]
    [-strand strand] [-parse_deflines] [-query_gencode int_value]
    [-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]
    [-comp_based_stats compo] [-use_sw_tback] [-version]

DESCRIPTION
   Translated Query-Protein Subject BLAST 2.5.0+

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

[GenoMax]

That is because you are looking at task option for blastn -help which has

 -task <String, Permissible values: 'blastn' 'blastn-short' 'dc-megablast'
                'megablast' 'rmblastn' >

If you look at blastx -help you will see

 -task <String, Permissible values: 'blastx' 'blastx-fast' >
   Task to execute
   Default = `blastx'

[marongiu.luigi]

Yes thank you, I thought blastx was a task of blastn instead is another program altogether. I am running it now. case closed.