trimest
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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
Remove poly-A tails from nucleotide sequences
Version: EMBOSS:6.6.0.0
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
the 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
-scircular1 boolean Sequence is circular
-squick1 boolean Read id and sequence only
-sformat1 string Input sequence format
-iquery1 string Input query fields or ID list
-ioffset1 integer Input start position offset
-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 and exit. 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
-version boolean Report version number and exit
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 INSDC.
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 sequence in the Finkel-Biskis-Reilly murine sarcoma virus";
RL Oncogene 8(9):2537-2546(1993).
XX
DR Ensembl-Gn; ENSG00000149806; Homo_sapiens.
DR Ensembl-Tr; ENST00000279259; Homo_sapiens.
DR Ensembl-Tr; ENST00000434372; Homo_sapiens.
DR Ensembl-Tr; ENST00000525297; Homo_sapiens.
DR Ensembl-Tr; ENST00000526555; Homo_sapiens.
DR Ensembl-Tr; ENST00000527548; Homo_sapiens.
DR Ensembl-Tr; ENST00000529259; Homo_sapiens.
DR Ensembl-Tr; ENST00000529639; Homo_sapiens.
DR Ensembl-Tr; ENST00000531743; Homo_sapiens.
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="H-InvDB:HIT000322806.14"
FT /db_xref="HGNC:3597"
FT /db_xref="InterPro:IPR000626"
FT /db_xref="InterPro:IPR006846"
FT /db_xref="InterPro:IPR019954"
FT /db_xref="InterPro:IPR019955"
FT /db_xref="InterPro:IPR019956"
FT /db_xref="PDB:2L7R"
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 sequence 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
None.
Diagnostic Error Messages
None.
Exit status
It always exits with status 0.
Known bugs
None.
See also
Program name Description
aligncopy Read and write alignments
aligncopypair Read and write pairs from alignments
biosed Replace or delete sequence sections
codcopy Copy and reformat a codon usage table
cutseq Remove a section from a sequence
degapseq Remove non-alphabetic (e.g. gap) characters from sequences
descseq Alter the name or description of a sequence
entret Retrieve 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 Read and write a feature table
featmerge Merge two overlapping feature tables
featreport Read and write a feature table
feattext Return a feature table original text
listor Write a list file of the logical OR of two sets of sequences
makenucseq Create random nucleotide sequences
makeprotseq Create random protein sequences
marscan Find matrix/scaffold recognition (MRS) signatures in DNA
sequences
maskambignuc Mask all ambiguity characters in nucleotide sequences with
N
maskambigprot Mask 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 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
nthseqset Read and write (return) one set of sequences from many
pasteseq Insert one sequence into another
revseq Reverse and complement a nucleotide sequence
seqcount Read and count sequences
seqret Read and write (return) sequences
seqretsetall Read and write (return) many sets of sequences
seqretsplit Read sequences and write them to individual files
sirna Find siRNA duplexes in mRNA
sizeseq Sort sequences by size
skipredundant Remove redundant sequences from an input set
skipseq Read and write (return) sequences, skipping first few
splitsource Split sequence(s) into original source sequences
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 Remove vectors from the ends of nucleotide sequence(s)
yank Add a sequence reference (a full USA) to a list file
Author(s)
Gary Williams formerly at:
MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust
Genome Campus, Hinxton, Cambridge, CB10 1SB, UK
Please report all bugs to the EMBOSS bug team
(emboss-bug (c) emboss.open-bio.org) not to the original author.
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