| Description |
TRIMSEQ application details page
Trim ambiguous bits off the ends of sequences
This program is used to tidy up the ends of sequences, removing allthe bits that you would really rather were not published. Specifically, it: - removes all gap characters from the ends.
- removes X's and N's (in nucleic sequences) from the ends.
- optionally removes *'s from the ends
- optionally removes IUPAC ambiguity codes from the ends (B and Z in proteins, M,R,W,S,Y,K,V,H,D and B in nucleic sequences)
It then optionally trims off poor quality regions from the end, usinga threshold percentage of unwanted characters in a window which is movedalong the sequence from the ends. The unwanted characters which are usedare X's and N's (in nucleic sequences), optionally *'s, and optionallyIUPAC ambiguity codes. The program stops trimming the ends when the percentage ofunwanted characters in the moving window drops below thethreshold percentage. Thus if the window size is set to 1 and the percentage thresholdis 100, no further poor quality regions will be removed.If the window size is set to 5 and the percentage threshold is 40then the sequence AAGCTNNNNATT will be trimmed to AAGCT,while AAGCTNATT or AAGCTNNNNATTT will not be trimmed as less than40% of the last 5 characters are N's. After trimming these poor quality regions, it will again thentrim off any dangling gap characters from the ends .
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