Finding Patterns Using the Smith-Waterman Algorithm

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.

Parameters:

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:

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

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

The following values are available:

Example:

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