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TRIMEST(1e) EMBOSS Manual for Debian TRIMEST(1e)

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 preceeding 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.

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