TRIMSEQ(1e) | EMBOSS Manual for Debian | TRIMSEQ(1e) |
NAME¶
trimseq - Remove unwanted characters from start and end of sequence(s)SYNOPSIS¶
trimseq -sequence seqall [-window integer] [-percent float] [-strict boolean] [-star boolean] -left boolean -right boolean -outseq seqoutall
trimseq -help
DESCRIPTION¶
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 seqallAdditional section¶
-window integerThis 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 booleanDefault value: Y
-right boolean
Default value: Y
Output section¶
-outseq seqoutallBUGS¶
Bugs can be reported to the Debian Bug Tracking system (http://bugs.debian.org/emboss), or directly to the EMBOSS developers (http://sourceforge.net/tracker/?group_id=93650&atid=605031).SEE ALSO¶
trimseq is fully documented via the tfm(1) system.AUTHOR¶
Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>Wrote the script used to autogenerate this manual
page.
COPYRIGHT¶
This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package. It can be redistributed under the same terms as EMBOSS itself.
05/11/2012 | EMBOSS 6.4.0 |