EMBOSS: trimest

| trimest

## Function

Remove poly-A tails from nucleotide sequences

## Description

trimest reads one or more nucleotide sequences and writes them out again but with any 3' poly-A tail (or, optionally, 5' poly-T tail) removed. It detect any poly-A and poly-T tails in the input sequences that are at least the specified minimum length. The tails may continue a defined num of non-A or non-T bases. If both a 5' poly-T tail and a 3' poly-A tail is identified, it removes the longest of the two. 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.

## Algorithm

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.

## Usage

Here is a sample session with trimest

    % trimest tembl:x65923 x65923.seq
    Remove poly-A tails from nucleotide 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     Nucleotide sequence(s) filename and optional
                                      format, or reference (input USA)
      [-outseq]            seqoutall  [.] Sequence set(s)
                                      filename and optional format (output USA)

       Additional (Optional) qualifiers:
       -minlength          integer    [4] 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)
       -mismatches         integer    [1] 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)
       -[no]reverse        boolean    [Y] 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     [N] 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    [Y] 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 first file to standard output
       -filter             boolean    Read first file from standard input, write
                                      first file to 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 dying program messages

Standard (Mandatory) qualifiers | Allowed values | Default
--- | --- | ---
[-sequence] (Parameter 1) | Nucleotide sequence(s) filename and optional format, or reference (input USA) | Readable sequence(s) | Required
[-outseq] (Parameter 2) | Sequence set(s) filename and optional format (output USA) | Writeable sequence(s) | <*>.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:x65923' is a sequence entry in the example nucleic acid database 'tembl'

### Database entry: tembl:x65923

    ID   X65923; SV 1; linear; mRNA; STD; HUM; 518 BP.
    XX
    AC   X65923;
    XX
    DT   13-MAY-1992 (Rel. 31, Created)
    DT   18-APR-2005 (Rel. 83, Last updated, Version 11)
    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; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae;
    OC   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   PUBMED; 8395683.
    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(9):2537-2546(1993).
    XX
    DR   H-InvDB; HIT000322806.
    XX
    FH   Key             Location/Qualifiers
    FH
    FT   source          1..518
    FT                   /organism="Homo sapiens"
    FT                   /chromosome="11q"
    FT                   /map="13"
    FT                   /mol_type="mRNA"
    FT                   /clone_lib="cDNA"
    FT                   /clone="pUIA 631"
    FT                   /tissue_type="placenta"
    FT                   /db_xref="taxon:9606"
    FT   misc_feature    57..278
    FT                   /note="ubiquitin like part"
    FT   CDS             57..458
    FT                   /gene="fau"
    FT                   /db_xref="GDB:135476"
    FT                   /db_xref="GOA:P35544"
    FT                   /db_xref="GOA:P62861"
    FT                   /db_xref="HGNC:3597"
    FT                   /db_xref="UniProtKB/Swiss-Prot:P35544"
    FT                   /db_xref="UniProtKB/Swiss-Prot:P62861"
    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

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.

### Output files for usage example

### File: x65923.seq

    >X65923 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

EST and mRNA sequences often have poly-A tails at their 3' end. Where an EST sequences is the reverse complement of a corresponding mRNA's forward sense it may have a poly-T tail at its 5' end.

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 (see "Algorithm").

## References

None.

## Warnings

trimest can make no guarantee that the tails removed have biologic significance or not. They may in fact be part of the transcribed sequence.

## Diagnostic Error Messages

None.

## Exit status

It always exits with status 0.

## Known bugs

None.

## See also

Program name | Description
--- | ---
aligncopy | Reads and writes alignments
aligncopypair | Reads and writes pairs from alignments
biosed | Replace or delete sequence sections
codcopy | Copy and reformat a codon usage table
cutseq | Removes a section from a sequence
degapseq | Removes non-alphabetic (e.g. gap) characters from sequences
descseq | Alter the name or description of a sequence
entret | Retrieves sequence entries from flatfile databases and files
extractalign | Extract regions from a sequence alignment
extractfeat | Extract features from sequence(s)
extractseq | Extract regions from a sequence
featcopy | Reads and writes a feature table
featreport | Reads and writes a feature table
listor | Write a list file of the logical OR of two sets of sequences
makenucseq | Create random nucleotide sequences
makeprotseq | Create random protein sequences
maskambignuc | Masks all ambiguity characters in nucleotide sequences with N
maskambigprot | Masks all ambiguity characters in protein sequences with X
maskfeat | Write a sequence with masked features
maskseq | Write a sequence with masked regions
newseq | Create a sequence file from a typed-in sequence
nohtml | Remove mark-up (e.g. HTML tags) from an ASCII text file
noreturn | Remove carriage return from ASCII files
nospace | Remove all whitespace from an ASCII text file
notab | Replace tabs with spaces in an ASCII text file
notseq | Write to file a subset of an input stream of sequences
nthseq | Write to file a single sequence from an input stream of sequences
pasteseq | Insert one sequence into another
revseq | Reverse and complement a nucleotide sequence
seqret | Reads and writes (returns) sequences
seqretsplit | Reads sequences and writes them to individual files
sizeseq | Sort sequences by size
skipredundant | Remove redundant sequences from an input set
skipseq | Reads and writes (returns) sequences, skipping first few
splitter | Split sequence(s) into smaller sequences
trimseq | Remove unwanted characters from start and end of sequence(s)
trimspace | Remove extra whitespace from an ASCII text file
union | Concatenate multiple sequences into a single sequence
vectorstrip | Removes vectors from the ends of nucleotide sequence(s)
yank | Add a sequence reference (a 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