xenial (1) trimest.1e.gz

Provided by: emboss_6.6.0+dfsg-3build1_amd64 bug

NAME

       trimest - Remove poly-A tails from nucleotide sequences

SYNOPSIS

       trimest -sequence seqall [-minlength integer] [-mismatches integer] [-reverse boolean] [-tolower toggle]
               -fiveprime boolean -outseq seqoutall

       trimest -help

DESCRIPTION

       trimest is a command line program from EMBOSS (“the European Molecular Biology Open Software Suite”). It
       is part of the "Nucleic:Functional sites,Edit" command group(s).

OPTIONS

   Input section
       -sequence seqall

   Additional section
       -minlength integer
           This is the minimum length that a poly-A (or poly-T) tail must have before it is removed. If there
           are mismatches in the tail than there must be at least this length of poly-A tail before the mismatch
           for the mismatch to be considered part of the tail. Default value: 4

       -mismatches integer
           If there are this number or fewer contiguous non-A bases in a poly-A tail then, if there are
           '-minlength' 'A' bases before them, they will be considered part of the tail and removed . For
           example the terminal 4 A's of GCAGAAAA would be removed with the default values of -minlength=4 and
           -mismatches=1 (There are not at least 4 A's before the last 'G' and so only the A's after it are
           considered to be part of the tail). The terminal 9 bases of GCAAAAGAAAA would be removed; There are
           at least -minlength A's preceding the last 'G', so it is part of the tail. Default value: 1

       -reverse boolean
           When a poly-T region at the 5' end of the sequence is found and removed, it is likely that the
           sequence is in the reverse sense. This option will change the sequence to the forward sense when it
           is written out. If this option is not set, then the sense will not be changed. Default value: Y

       -tolower toggle
           The poly-A region can be 'masked' by converting the sequence characters to lower-case. Some
           non-EMBOSS programs e.g. fasta can interpret this as a masked region. The sequence is unchanged apart
           from the case change. You might like to ensure that the whole sequence is in upper-case before
           masking the specified regions to lower-case by using the '-supper' sequence qualifier. Default value:
           N

   Advanced section
       -fiveprime boolean
           If this is set true, then the 5' end of the sequence is inspected for poly-T tails. These will be
           removed if they are longer than any 3' poly-A tails. If this is false, then the 5' end is ignored.
           Default value: Y

   Output section
       -outseq seqoutall

BUGS

       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

       trimest 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.

       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.