| 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 tembl:hsfau hsfau.seq
    Trim poly-A tails off EST sequences

Go to the input files for this example
Go to the output files for this example

## Command line arguments

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

       Additional (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        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.
       -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.

       Advanced (Unprompted) qualifiers:
       -[no]fiveprime      boolean    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.

       Associated qualifiers:

       "-sequence" associated qualifiers
       -sbegin1             integer    Start of each sequence to be used
       -send1               integer    End of each sequence to be used
       -sreverse1           boolean    Reverse (if DNA)
       -sask1               boolean    Ask for begin/end/reverse
       -snucleotide1        boolean    Sequence is nucleotide
       -sprotein1           boolean    Sequence is protein
       -slower1             boolean    Make lower case
       -supper1             boolean    Make upper case
       -sformat1            string     Input sequence format
       -sdbname1            string     Database name
       -sid1                string     Entryname
       -ufo1                string     UFO features
       -fformat1            string     Features format
       -fopenfile1          string     Features file name

       "-outseq" associated qualifiers
       -osformat2           string     Output seq format
       -osextension2        string     File name extension
       -osname2             string     Base file name
       -osdirectory2        string     Output directory
       -osdbname2           string     Database name to add
       -ossingle2           boolean    Separate file for each entry
       -oufo2               string     UFO features
       -offormat2           string     Features format
       -ofname2             string     Features file name
       -ofdirectory2        string     Output directory

       General qualifiers:
       -auto                boolean    Turn off prompts
       -stdout              boolean    Write standard output
       -filter              boolean    Read standard input, write standard output
       -options             boolean    Prompt for standard and additional values
       -debug               boolean    Write debug output to program.dbg
       -verbose             boolean    Report some/full command line options
       -help                boolean    Report command line options. More
                                      information on associated and general
                                      qualifiers can be found with -help -verbose
       -warning             boolean    Report warnings
       -error               boolean    Report errors
       -fatal               boolean    Report fatal errors
       -die                 boolean    Report deaths

Standard (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
Additional (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. | Boolean value Yes/No | Yes
-tolower | 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. | Toggle value Yes/No | No
Advanced (Unprompted) 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. | Boolean value Yes/No | Yes

## Input file format

trimest reads the USA of one or more normal nucleic acid sequences.

### Input files for usage example

'tembl:hsfau' is a sequence entry in the example nucleic acid database 'tembl'

### Database entry: tembl:hsfau

    ID   HSFAU      standard; RNA; HUM; 518 BP.
    XX
    AC   X65923;
    XX
    SV   X65923.1
    XX
    DT   13-MAY-1992 (Rel. 31, Created)
    DT   23-SEP-1993 (Rel. 37, Last updated, Version 10)
    XX
    DE   H.sapiens fau mRNA
    XX
    KW   fau gene.
    XX
    OS   Homo sapiens (human)
    OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
    OC   Eutheria; Primates; Catarrhini; Hominidae; Homo.
    XX
    RN   [1]
    RP   1-518
    RA   Michiels L.M.R.;
    RT   ;
    RL   Submitted (29-APR-1992) to the EMBL/GenBank/DDBJ databases.
    RL   L.M.R. Michiels, University of Antwerp, Dept of Biochemistry,
    RL   Universiteisplein 1, 2610 Wilrijk, BELGIUM
    XX
    RN   [2]
    RP   1-518
    RX   MEDLINE; 93368957.
    RA   Michiels L., Van der Rauwelaert E., Van Hasselt F., Kas K., Merregaert J.;
    RT   " fau cDNA encodes a ubiquitin-like-S30 fusion protein and is expressed as
    RT   an antisense sequences in the Finkel-Biskis-Reilly murine sarcoma virus";
    RL   Oncogene 8:2537-2546(1993).
    XX
    DR   SWISS-PROT; P35544; UBIM_HUMAN.
    DR   SWISS-PROT; Q05472; RS30_HUMAN.
    XX
    FH   Key             Location/Qualifiers
    FH
    FT   source          1..518
    FT                   /chromosome="11q"
    FT                   /db_xref="taxon:9606"
    FT                   /organism="Homo sapiens"
    FT                   /tissue_type="placenta"
    FT                   /clone_lib="cDNA"
    FT                   /clone="pUIA 631"
    FT                   /map="13"
    FT   misc_feature    57..278
    FT                   /note="ubiquitin like part"
    FT   CDS             57..458
    FT                   /db_xref="SWISS-PROT:P35544"
    FT                   /db_xref="SWISS-PROT:Q05472"
    FT                   /gene="fau"
    FT                   /protein_id="CAA46716.1"
    FT                   /translation="MQLFVRAQELHTFEVTGQETVAQIKAHVASLEGIAPEDQVVLLAG
    FT                   APLEDEATLGQCGVEALTTLEVAGRMLGGKVHGSLARAGKVRGQTPKVAKQEKKKKKTG
    FT                   RAKRRMQYNRRFVNVVPTFGKKKGPNANS"
    FT   misc_feature    98..102
    FT                   /note="nucleolar localization signal"
    FT   misc_feature    279..458
    FT                   /note="S30 part"
    FT   polyA_signal    484..489
    FT   polyA_site      509
    XX
    SQ   Sequence 518 BP; 125 A; 139 C; 148 G; 106 T; 0 other;
         ttcctctttc tcgactccat cttcgcggta gctgggaccg ccgttcagtc gccaatatgc        60
         agctctttgt ccgcgcccag gagctacaca ccttcgaggt gaccggccag gaaacggtcg       120
         cccagatcaa ggctcatgta gcctcactgg agggcattgc cccggaagat caagtcgtgc       180
         tcctggcagg cgcgcccctg gaggatgagg ccactctggg ccagtgcggg gtggaggccc       240
         tgactaccct ggaagtagca ggccgcatgc ttggaggtaa agttcatggt tccctggccc       300
         gtgctggaaa agtgagaggt cagactccta aggtggccaa acaggagaag aagaagaaga       360
         agacaggtcg ggctaagcgg cggatgcagt acaaccggcg ctttgtcaac gttgtgccca       420
         cctttggcaa gaagaagggc cccaatgcca actcttaagt cttttgtaat tctggctttc       480
         tctaataaaa aagccactta gttcagtcaa aaaaaaaa                               518
    //

## Output file format

### Output files for usage example

### File: hsfau.seq

    >HSFAU X65923.1 H.sapiens fau mRNA [poly-A tail removed]
    ttcctctttctcgactccatcttcgcggtagctgggaccgccgttcagtcgccaatatgc
    agctctttgtccgcgcccaggagctacacaccttcgaggtgaccggccaggaaacggtcg
    cccagatcaaggctcatgtagcctcactggagggcattgccccggaagatcaagtcgtgc
    tcctggcaggcgcgcccctggaggatgaggccactctgggccagtgcggggtggaggccc
    tgactaccctggaagtagcaggccgcatgcttggaggtaaagttcatggttccctggccc
    gtgctggaaaagtgagaggtcagactcctaaggtggccaaacaggagaagaagaagaaga
    agacaggtcgggctaagcggcggatgcagtacaaccggcgctttgtcaacgttgtgccca
    cctttggcaagaagaagggccccaatgccaactcttaagtcttttgtaattctggctttc
    tctaataaaaaagccacttagttcagtc

The output is a set of sequences with the poly-A (or poly-T) tails removed. If a sequence had a 5' poly-T tail then the resulting sequence is reverse-complemented by default. The description line has a comment appended about the changes made to the sequence.

## 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
skipseq | Reads and writes (returns) sequences, skipping the first few
splitter | Split a sequence into (overlapping) smaller sequences
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)

Gary Williams (gwilliam © rfcgr.mrc.ac.uk)
MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, 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

None