This is the command trimeste that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
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
Use trimeste online using onworks.net services
