
                              EMBOSS: trimest
     _________________________________________________________________
   
                                Program trimest
                                       
Function

   Trim poly-A tails off EST sequences
   
Description

   EST and mRNA sequences often have poly-A tails at the end of them.
   This utility removes those poly-A tails.
   
   EST sequences are often the reverse complement of the corresponding
   mRNA's forward sense and have poly-T tails at their 5' end. By
   default, this program also detects and removes these and writes out
   the reverse complement of the sequence.
   
   trimest is not infallible. There are often repeats of 'A' (or 'T') in
   a sequence that just happen by chance to occur at the 3' (or 5') end
   of the EST sequence. trimest has no way of determining if the A's it
   finds are part of a real poly-A tail or are a part of the transcribed
   genomic sequence. It removes any apparent poly-A tails that match its
   criteria for a poly-A tail.
   
   trimest looks for a repeat of at least '-minlength' A's at the 3' end
   (and, by default, '-minlength' T's at the 5' end). If there are an
   apparent 5' poly-T tail and a poly-A tail, then it removes whichever
   is the longer of the two.
   
   By default, it will allow '-mismatches' non-A (or non-T) bases in the
   tail. If a mismatch is found, then there has to be at least
   '-minlength' A's (or T's) past the mismatch (working from the end) for
   the mismatch to be considered part of the tail. If '-mismatches' is
   greater than 1 then that number of contiguous non-A (or non-T) bases
   will be allowed as part of the tail.
   
   If a 5' poly-T tail is found, then the sequence will be optionally
   reverse-complemented when it is written out.
   
   If a poly-A tail is reomved then '[poly-A tail removed]' is appended
   to the description of the sequence. If poly-T is removed, then
   '[poly-T tail removed]' is appended and if the sequence is reversed,
   '[reverse complement]' is appended.
   
Usage

   Here is a sample session with trimest:

% trimest embl:hsfau hsfau.seq

Command line arguments

   Mandatory qualifiers:
  [-sequence]          seqall     Sequence database USA
  [-outseq]            seqoutall  Output sequence(s) USA

   Optional qualifiers:
   -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.
   -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.
   -[no]reverse        bool       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.

   Advanced qualifiers:
   -[no]fiveprime      bool       If this is set true, then the 5' end of teh
                                  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.

   General qualifiers:
  -help                bool       report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   

   Mandatory qualifiers Allowed values Default
   [-sequence]
   (Parameter 1) Sequence database USA Readable sequence(s) Required
   [-outseq]
   (Parameter 2) Output sequence(s) USA Writeable sequence(s)
   <sequence>.format
   Optional qualifiers Allowed values Default
   -minlength 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. Integer 1
   or more 4
   -mismatches 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. Integer 0 or more
   1
   -[no]reverse 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. Yes/No Yes
   Advanced qualifiers Allowed values Default
   -[no]fiveprime If this is set true, then the 5' end of teh 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. Yes/No Yes
   
Input file format

   Normal nucleic acid sequences USA.
   
Output file format

   The output is a set of sequences with the poly-A (or poly-T) tails
   removed. If the sequences had a 5' poly-T tail then are
   reverse-complemented by default. The description line has a comment
   appended about the changes made to the sequence.
   
   For example, the sequence embl:hsfau is written out as:
     _________________________________________________________________
   
>HSFAU X65923 H.sapiens fau mRNA [poly-A tail removed]
ttcctctttctcgactccatcttcgcggtagctgggaccgccgttcagtcgccaatatgc
agctctttgtccgcgcccaggagctacacaccttcgaggtgaccggccaggaaacggtcg
cccagatcaaggctcatgtagcctcactggagggcattgccccggaagatcaagtcgtgc
tcctggcaggcgcgcccctggaggatgaggccactctgggccagtgcggggtggaggccc
tgactaccctggaagtagcaggccgcatgcttggaggtaaagttcatggttccctggccc
gtgctggaaaagtgagaggtcagactcctaaggtggccaaacaggagaagaagaagaaga
agacaggtcgggctaagcggcggatgcagtacaaccggcgctttgtcaacgttgtgccca
cctttggcaagaagaagggccccaatgccaactcttaagtcttttgtaattctggctttc
tctaataaaaaagccacttagttcagtc
     _________________________________________________________________
   
Data files

   None.
   
Notes

   None.
   
References

   None.
   
Warnings

   It will trim any run of more than -minlength A's or T's at the 3' or
   5' end, whether or not they are a true poly-A tail.
   
Diagnostic Error Messages

   None.
   
Exit status

   It always exits with status 0.
   
Known bugs

   None.
   
See also

   Program name                          Description
   biosed       Replace or delete sequence sections
   cutseq       Removes a specified section from a sequence
   degapseq     Removes gap characters from sequences
   descseq      Alter the name or description of a sequence
   entret       Reads and writes (returns) flatfile entries
   extractfeat  Extract features from a sequence
   extractseq   Extract regions from a sequence
   listor       Writes a list file of the logical OR of two sets of sequences
   maskfeat     Mask off features of a sequence
   maskseq      Mask off regions of a sequence
   newseq       Type in a short new sequence
   noreturn     Removes carriage return from ASCII files
   notseq       Excludes a set of sequences and writes out the remaining ones
   nthseq       Writes one sequence from a multiple set of sequences
   pasteseq     Insert one sequence into another
   revseq       Reverse and complement a sequence
   seqret       Reads and writes (returns) sequences
   seqretsplit  Reads and writes (returns) sequences in individual files
   splitter     Split a sequence into (overlapping) smaller sequences
   swissparse   Retrieves sequences from swissprot using keyword search
   trimseq      Trim ambiguous bits off the ends of sequences
   union        Reads sequence fragments and builds one sequence
   vectorstrip  Strips out DNA between a pair of vector sequences
   yank         Reads a sequence range, appends the full USA to a list file
   
Author(s)

   This application was written by Gary Williams
   (gwilliam@hgmp.mrc.ac.uk)
   
History

   Written (3 Oct 2001) - Gary Williams
   
Target users

   This program is intended to be used by everyone and everything, from
   naive users to embedded scripts.
   
Comments
