SYNOPSIS

trimseq -sequence seqall [-window integer] [-percent float] [-strict boolean] [-star boolean] -left boolean -right boolean -outseq seqoutall

trimseq -help

DESCRIPTION

trimseq

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

AUTHOR

Debian Med Packaging Team <[email protected]>

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.