EMBOSS: trimest

| ## 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