Blast command use

Question

[harry]

Hi, I want to know how I used a {Somewhat similar sequences (blastn) } command in the BLAST command in Linux.

when I used blastn -h this help page open but that there is no command for somewhat similar sequences.

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] [-negative_seqidlist filename]
    [-taxids taxids] [-negative_taxids taxids] [-taxidlist filename]
    [-negative_taxidlist 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] [-subject_besthit]
    [-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] [-sorthits sort_hits]
    [-sorthsps sort_hsps] [-max_target_seqs num_sequences]
    [-num_threads int_value] [-remote] [-version]

Thanks in advance

Answer 1

[Mensur Dlakic]

Type blastn -help to get a more detailed help. The option you want will be invoked with -task blastn.

[harry]

thanks

[harry]

Is there any command to just get the output of 1st 2 queries not more than 2? Because after use of -task blastn command the file is making too much large so I want to make small file. So I just want to only 1st 2 queries which have the best e value and bit score have come in my output file. Thanks in advance

[Mensur Dlakic]

I told you how to get detailed help, so now it is just a matter of reading what's in it. Look into -num_descriptions, -num_alignments and -max_target_seqs options, all of which are fairly self-explanatory.