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