
                                  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

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="MQLFVRAQELHTFEVTGQETVAQIKAHVASLEGIAPEDQVVLLA
G
FT                   APLEDEATLGQCGVEALTTLEVAGRMLGGKVHGSLARAGKVRGQTPKVAKQEKKKKKT
G
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        6
0
     agctctttgt ccgcgcccag gagctacaca ccttcgaggt gaccggccag gaaacggtcg       12
0
     cccagatcaa ggctcatgta gcctcactgg agggcattgc cccggaagat caagtcgtgc       18
0
     tcctggcagg cgcgcccctg gaggatgagg ccactctggg ccagtgcggg gtggaggccc       24
0
     tgactaccct ggaagtagca ggccgcatgc ttggaggtaa agttcatggt tccctggccc       30
0
     gtgctggaaa agtgagaggt cagactccta aggtggccaa acaggagaag aagaagaaga       36
0
     agacaggtcg ggctaagcgg cggatgcagt acaaccggcg ctttgtcaac gttgtgccca       42
0
     cctttggcaa gaagaagggc cccaatgcca actcttaagt cttttgtaat tctggctttc       48
0
     tctaataaaa aagccactta gttcagtcaa aaaaaaaa                               51
8
//

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
