trimseq1e
Remove unwanted characters from start and end of sequence(s)
Usage
trimseq -sequence
seqall
[-window
integer]
[-percent
float]
[-strict
boolean]
[-star
boolean]
-left
boolean
-right
boolean
-outseq
seqoutall
trimseq -help
Overview
trimseq is a command line program from EMBOSS (“the European Molecular Biology Open Software Suite”). It is part of the "Edit" command group(s).
Options
Input section
-
-sequence seqall
Additional section
-
-window integer -
This determines the size of the region that is considered when deciding whether the percentage of ambiguity is greater than the threshold. A value of 5 means that a region of 5 letters in the sequence is shifted along the sequence from the ends and trimming is done only if there is a greater or equal percentage of ambiguity than the threshold percentage. Default value: 1
-
-percent float -
This is the threshold of the percentage ambiguity in the window required in order to trim a sequence. Default value: 100.0
-
-strict boolean -
In nucleic sequences, trim off not only N's and X's, but also the nucleotide IUPAC ambiguity codes M, R, W, S, Y, K, V, H, D and B. In protein sequences, trim off not only X's but also B and Z. Default value: N
-
-star boolean -
In protein sequences, trim off not only X's, but also the *'s Default value: N
Advanced section
-
-left boolean -
Default value: Y
-
-right boolean -
Default value: Y
Output section
-
-outseq seqoutall
Releases
9 releases since Debian 5.0 (Lenny); the text changed 2 times.