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¶
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
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.
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.