Ncbi Blast Command Line Align Two Sequences
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8.1 years ago
Maria ▴ 170

I want to align 2 sequences using ncbi blast command line or bioperl script, I am new to blast and I found out that it compare a sequence to a database but what I need it to compare two sequences like in the web service . how to do it ? Thanks in advance

blast • 18k views
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blastn -query file1.fa -subject file2.fa
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The same 2 files when I use as input in the web service I got a result but when I use this command it gives me NO hits found

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try to add the option -dust no, -expect 10 (I think that's the syntax. Anyway, you can get the help with blastn -help )

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hello sir i am trying this command for my task. but still terminal show error. which i shown below. please ckeck this and help me to solve out this error codon@codon-PC-MY18XRZE4:~/ncbi-blast-2.6.0+/c++/ReleaseMT/build$ blastn -yasl2 variant x1.fasta -sra_data.fasta 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] [-xdrop_ungap float_value] [-xdrop_gap float_value] [-xdrop_gap_final float_value] [-searchsp int_value] [-max_hsps_per_subject int_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] [-html] [-max_target_seqs num_sequences] [-num_threads int_value] [-remote] [-version]

DESCRIPTION Nucleotide-Nucleotide BLAST 2.2.28+

Use '-help' to print detailed descriptions of command line arguments

Error: Unknown argument: "yasl2"

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Blast Two Sequences

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