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  • Finding Pattern Using Smith-Waterman Algorithm
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Task Name: find-sw

Searches for a pattern in a nucleotide or protein sequence using the Smith-Waterman algorithm and saves the regions found as annotations.


in — input sequence file. [String, Required]

out — output file with the annotations. [String, Required]

name — name of the annotated regions. [String, Optional, Default: “misc_feature”]

ptrn — subsequence pattern to search for (e.g. AGGCCT). [String, Required]

score — percent identity between the pattern and a subsequence. [Number, Optional, Default: 90]

matrix — scoring matrix. [String, Optional, Default: “Auto”]

Among others the following values are available:

    • blosum62
    • dna
    • rna
    • dayhoff
    • gonnet
    • pam250
    • etc.

The matrices available are stored in the $UGENE\data\weight_matrix directory.

filter — results filtering strategy. [String, Optional, Default: “filter-intersections”]

The following values are available:

    • filter-intersections
    • none


ugene find-sw --in=human_T1.fa --ptrn=TGCT --filter=none
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