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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:x65923 x65923.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 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 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 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
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
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
extractalign Extract regions from a sequence alignment
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
makenucseq Creates random nucleotide sequences
makeprotseq Creates random protein 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
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