
                              EMBOSS: trimseq
     _________________________________________________________________
   
                                Program trimseq
                                       
Function

   Trim ambiguous bits off the ends of sequences
   
Description

   This program is used to tidy up the ends of sequences, removing all
   the bits that you would really rather were not published.
   
   Specifically, it:
     * removes all gap characters from the ends.
     * removes X's and N's (in nucleic sequences) from the ends.
     * optionally removes *'s from the ends
     * optionally removes IUPAC ambiguity codes from the ends (B and Z in
       proteins, M,R,W,S,Y,K,V,H,D and B in nucleic sequences)
       
   It then optionally trims off poor quality regions from the end, using
   a threshold percentage of unwanted characters in a window which is
   moved along the sequence from the ends. The unwanted characters which
   are used are X's and N's (in nucleic sequences), optionally *'s, and
   optionally IUPAC ambiguity codes.
   
   The program stops trimming the ends when the percentage of unwanted
   characters in the moving window drops below the threshold percentage.
   
   Thus if the window size is set to 1 and the percentage threshold is
   100, no further poor quality regions will be removed. If the window
   size is set to 5 and the percentage threshold is 40 then the sequence
   AAGCTNNNNATT will be trimmed to AAGCT, while AAGCTNATT or
   AAGCTNNNNATTT will not be trimmed as less than 40% of the last 5
   characters are N's.
   
   After trimming these poor quality regions, it will again then trim off
   any dangling gap characters from the ends .
   
Usage

   Tidy up the sequence ends, stopping at the first wanted code
% trimseq xyz.seq xyz_clean.seq -window 1 -percent 100

   Tidy up the sequence ends, removing poor bits at the ends
% trimseq xyz.seq xyz_clean.seq -window 5 -percent 40

   Tidy up the sequence ends, removing very poor bits at the ends
% trimseq xyz.seq xyz_clean.seq -window 20 -percent 80

   Tidy up the sequence ends, removing even maginally poor bits at the
   ends
% trimseq xyz.seq xyz_clean.seq -window 20 -percent 10

   Tidy up the sequence ends, removing poor bits including ambiguity
   codes
% trimseq xyz.seq xyz_clean.seq -window 20 -percent 50 -strict

   Tidy up the sequence ends, removing asterisks from a protein end
% trimseq xyz.seq xyz_clean.seq -window 1 -percent 100 -star

   Tidy up the sequence ends, removing poor bits at only the left end
% trimseq xyz.seq xyz_clean.seq -window 20 -percent 50 -noright

Command line arguments

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

   Optional qualifiers:
   -window             integer    This determines the size of the region that
                                  is considered when deciding whether the
                                  percentage of ambiguity is greater than the
                                  threshold. A value of 5 means that a region
                                  of 5 letters in the sequence is shifted
                                  along the sequence from the ends and
                                  trimming is done only if there is a greater
                                  or equal percentage of ambiguity than the
                                  threshold percentage.
   -percent            float      This is the threshold of the percentage
                                  ambiguity in the window required in order to
                                  trim a sequence.
   -strict             bool       In nucleic sequences, trim off not only N's
                                  and X's, but also the nucleotide IUPAC
                                  ambiguity codes M, R, W, S, Y, K, V, H, D
                                  and B. In protein sequences, trim off not
                                  only X's but also B and Z.
   -star               bool       In protein sequences, trim off not only X's,
                                  but also the *'s

   Advanced qualifiers:
   -[no]left           bool       Trim at the start
   -[no]right          bool       Trim at the end

   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
   -window This determines the size of the region that is considered when
   deciding whether the percentage of ambiguity is greater than the
   threshold. A value of 5 means that a region of 5 letters in the
   sequence is shifted along the sequence from the ends and trimming is
   done only if there is a greater or equal percentage of ambiguity than
   the threshold percentage. Any integer value 1
   -percent This is the threshold of the percentage ambiguity in the
   window required in order to trim a sequence. Any integer value 100.0
   -strict In nucleic sequences, trim off not only N's and X's, but also
   the nucleotide IUPAC ambiguity codes M, R, W, S, Y, K, V, H, D and B.
   In protein sequences, trim off not only X's but also B and Z. Yes/No
   No
   -star In protein sequences, trim off not only X's, but also the *'s
   Yes/No No
   Advanced qualifiers Allowed values Default
   -[no]left Trim at the start Yes/No Yes
   -[no]right Trim at the end Yes/No Yes
   
Input file format

   Normal sequence.
   
Output file format

   Normal sequence file.
   
Data files

   None.
   
Notes

   If you use the '-star' qualifier and set the window size to greater
   than 1, you may trim bits of sequence with internal *'s. This may not
   be what you expected.
   
References

   None.
   
Warnings

   None.
   
Diagnostic Error Messages

   None.
   
Exit status

   It always exits with status 0.
   
Known bugs

   None noted.
   
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
   trimest      Trim poly-A tails off EST 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

   Finished.
   
Target users

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