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:

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


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 nameDescription
cutseqRemoves a specified section from a sequence
descseqAlter the name or description of a sequence
extractseqExtract regions from a sequence
maskfeatMask off features of a sequence
maskseqMask off regions of a sequence
megamergerMerge two large overlapping nucleic acid sequences
mergerMerge two overlapping nucleic acid sequences
newseqType in a short new sequence
noreturnRemoves carriage return from ASCII files
nthseqWrites one sequence from a multiple set of sequences
pasteseqInsert one sequence into another
revseqReverse and complement a sequence
splitterSplit a sequence into (overlapping) smaller sequences
vectorstripStrips out DNA between a pair of vector sequences

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