
                                  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="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

  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
   codcopy      Reads and writes a codon usage table
   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       Write 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       Exclude a set of sequences and write 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 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
