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tcode
Wiki
The master copies of EMBOSS documentation are available at
http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki.
Please help by correcting and extending the Wiki pages.
Function
Identify protein-coding regions using Fickett TESTCODE statistic
Description
tcode identifies protein-coding regions in one or more DNA sequences
using the fickett TESTCODE statistic. This is based on simple and
universal differences between protein-coding and noncoding DNA. The
TESTCODE statistic is calculated for windows of a specified size over
each input sequence. The results can be output as a standard EMBOSS
report file or displayed graphically.
The output reports each window as "Coding", "Noncoding" or "No
opinion". Entries marked "No opinion" have a TESTCODE value that falls
between the maximum and minimum values required to report a region as
noncoding or coding. For the graphical plot, all points above a green
horizontal line are determined to be coding regions. Those below a red
line are determined to be noncoding. Points between the red and green
lines are "no opinion" ones.
Biological Relevance
The statistic reflects the fact that codons are used with unequal
frequency and that oligonucleotides and nucleotides tend to be repeated
with a periodicity of three.
This application can assist in determining the probability of a region
of nucleic sequence encoding a functional protein.
Algorithm
The Fickett (1982) algorithm is used (1).
A window of at least 200 bases is moved over the sequence in steps of 3
bases
Let:
A1 = Number of A's in positions 1,4,7 ...
A2 = Number of A's in positions 2,5,8 ...
A3 = Number of A's in positions 3,6,9 ...
A position value is determined that reflects the degree to which each
base is favoured in one codon position over another, i.e.
Apos = MAX(A1,A2,A3) / MIN(A1,A2,A3)+1
This is done for all 4 bases. The percentage composition of each base
is also determined. Eight values are therefore determined, four
position values and four composition values. These are then converted
to probabilities (p) of coding using a look-up table provided as the
data file for the program. The values in this look-up table have been
determined experimentally using known coding and noncoding sequences.
Each of the probabilities is multiplied by a weight (w) value (again
from the look-up table) for the respective base. The weight value
reflects the percentage of the time that each parameter alone
successfully predicted coding or noncoding function for the sequences
of known function.
The TESTCODE statistic is then:
p1w1 + p2w2 + p3w3 + p4w4 + p5w5 + p6w6 + p7w7 + p8w8
A result of less than 0.74 is probably a non-coding region.
A result equal or greater than 0.95 is probably a coding region.
Anything in between these two values is uncertain.
Usage
Here is a sample session with tcode
% tcode
Identify protein-coding regions using Fickett TESTCODE statistic
Input nucleotide sequence(s): tembl:x65921
Length of sliding window [200]:
Output report [x65921.tcode]:
Go to the input files for this example
Go to the output files for this example
Example 2
Produce a graphical plot
% tcode -plot -graph cps
Identify protein-coding regions using Fickett TESTCODE statistic
Input nucleotide sequence(s): tembl:x65921
Length of sliding window [200]:
Created tcode.ps
Go to the output files for this example
Command line arguments
Identify protein-coding regions using Fickett TESTCODE statistic
Version: EMBOSS:6.6.0.0
Standard (Mandatory) qualifiers (* if not always prompted):
[-sequence] seqall Nucleotide sequence(s) filename and optional
format, or reference (input USA)
-window integer [200] This is the number of nucleotide bases
over which the TESTCODE statistic will be
performed each time. The window will then
slide along the sequence, covering the same
number of bases each time. (Integer 200 or
more)
* -outfile report [*.tcode] Output report file name (default
-rformat table)
* -graph xygraph [$EMBOSS_GRAPHICS value, or x11] Graph type
(ps, hpgl, hp7470, hp7580, meta, cps, x11,
tek, tekt, none, data, xterm, png, gif, pdf,
svg)
Additional (Optional) qualifiers: (none)
Advanced (Unprompted) qualifiers:
-datafile datafile [Etcode.dat] The default data file is
Etcode.dat and contains coding probabilities
for each base. The probabilities are for
both positional and compositional
information.
-step integer [3] The selected window will, by default,
slide along the nucleotide sequence by three
bases at a time, retaining the frame
(although the algorithm is not frame
sensitive). This may be altered to increase
or decrease the increment of the slide.
(Integer 1 or more)
-plot toggle [N] On selection a graph of the sequence (X
axis) plotted against the coding score (Y
axis) will be displayed. Sequence above the
green line is coding, that below the red
line is non-coding.
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
"-outfile" associated qualifiers
-rformat string Report format
-rname string Base file name
-rextension string File name extension
-rdirectory string Output directory
-raccshow boolean Show accession number in the report
-rdesshow boolean Show description in the report
-rscoreshow boolean Show the score in the report
-rstrandshow boolean Show the nucleotide strand in the report
-rusashow boolean Show the full USA in the report
-rmaxall integer Maximum total hits to report
-rmaxseq integer Maximum hits to report for one sequence
"-graph" associated qualifiers
-gprompt boolean Graph prompting
-gdesc string Graph description
-gtitle string Graph title
-gsubtitle string Graph subtitle
-gxtitle string Graph x axis title
-gytitle string Graph y axis title
-goutfile string Output file for non interactive displays
-gdirectory 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
The input is a standard EMBOSS sequence query (also known as a 'USA').
Major sequence database sources defined as standard in EMBOSS
installations include srs:embl, srs:uniprot and ensembl
Data can also be read from sequence output in any supported format
written by an EMBOSS or third-party application.
The input format can be specified by using the command-line qualifier
-sformat xxx, where 'xxx' is replaced by the name of the required
format. The available format names are: gff (gff3), gff2, embl (em),
genbank (gb, refseq), ddbj, refseqp, pir (nbrf), swissprot (swiss, sw),
dasgff and debug.
See: http://emboss.sf.net/docs/themes/SequenceFormats.html for further
information on sequence formats.
The program will ignore ambiguity codes in the nucleic acid sequence
and just accept the four common bases. This is a function of the
algorithm, and the data tables.
Input files for usage example
'tembl:x65921' is a sequence entry in the example nucleic acid database
'tembl'
Database entry: tembl:x65921
ID X65921; SV 1; linear; genomic DNA; STD; HUM; 2016 BP.
XX
AC X65921; S45242;
XX
DT 13-MAY-1992 (Rel. 31, Created)
DT 14-NOV-2006 (Rel. 89, Last updated, Version 7)
XX
DE H.sapiens fau 1 gene
XX
KW fau 1 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 1-2016
RA Kas K.;
RT ;
RL Submitted (29-APR-1992) to the INSDC.
RL K. Kas, University of Antwerp, Dept of Biochemistry T3.22,
RL Universiteitsplein 1, 2610 Wilrijk, BELGIUM
XX
RN [2]
RP 1-2016
RX DOI; 10.1016/0006-291X(92)91286-Y.
RX PUBMED; 1326960.
RA Kas K., Michiels L., Merregaert J.;
RT "Genomic structure and expression of the human fau gene: encoding the
RT ribosomal protein S30 fused to a ubiquitin-like protein";
RL Biochem. Biophys. Res. Commun. 187(2):927-933(1992).
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.
DR GDB; 191789.
DR GDB; 191790.
DR GDB; 354872.
DR GDB; 4590236.
XX
FH Key Location/Qualifiers
FH
FT source 1..2016
[Part of this file has been deleted for brevity]
FT RAKRRMQYNRRFVNVVPTFGKKKGPNANS"
FT intron 857..950
FT /number=2
FT exon 951..1095
FT /number=3
FT intron 1096..1556
FT /number=3
FT exon 1557..1612
FT /number=4
FT intron 1613..1786
FT /number=4
FT exon 1787..>1912
FT /number=5
FT polyA_signal 1938..1943
XX
SQ Sequence 2016 BP; 421 A; 562 C; 538 G; 495 T; 0 other;
ctaccatttt ccctctcgat tctatatgta cactcgggac aagttctcct gatcgaaaac 60
ggcaaaacta aggccccaag taggaatgcc ttagttttcg gggttaacaa tgattaacac 120
tgagcctcac acccacgcga tgccctcagc tcctcgctca gcgctctcac caacagccgt 180
agcccgcagc cccgctggac accggttctc catccccgca gcgtagcccg gaacatggta 240
gctgccatct ttacctgcta cgccagcctt ctgtgcgcgc aactgtctgg tcccgccccg 300
tcctgcgcga gctgctgccc aggcaggttc gccggtgcga gcgtaaaggg gcggagctag 360
gactgccttg ggcggtacaa atagcaggga accgcgcggt cgctcagcag tgacgtgaca 420
cgcagcccac ggtctgtact gacgcgccct cgcttcttcc tctttctcga ctccatcttc 480
gcggtagctg ggaccgccgt tcaggtaaga atggggcctt ggctggatcc gaagggcttg 540
tagcaggttg gctgcggggt cagaaggcgc ggggggaacc gaagaacggg gcctgctccg 600
tggccctgct ccagtcccta tccgaactcc ttgggaggca ctggccttcc gcacgtgagc 660
cgccgcgacc accatcccgt cgcgatcgtt tctggaccgc tttccactcc caaatctcct 720
ttatcccaga gcatttcttg gcttctctta caagccgtct tttctttact cagtcgccaa 780
tatgcagctc tttgtccgcg cccaggagct acacaccttc gaggtgaccg gccaggaaac 840
ggtcgcccag atcaaggtaa ggctgcttgg tgcgccctgg gttccatttt cttgtgctct 900
tcactctcgc ggcccgaggg aacgcttacg agccttatct ttccctgtag gctcatgtag 960
cctcactgga gggcattgcc ccggaagatc aagtcgtgct cctggcaggc gcgcccctgg 1020
aggatgaggc cactctgggc cagtgcgggg tggaggccct gactaccctg gaagtagcag 1080
gccgcatgct tggaggtgag tgagagagga atgttctttg aagtaccggt aagcgtctag 1140
tgagtgtggg gtgcatagtc ctgacagctg agtgtcacac ctatggtaat agagtacttc 1200
tcactgtctt cagttcagag tgattcttcc tgtttacatc cctcatgttg aacacagacg 1260
tccatgggag actgagccag agtgtagttg tatttcagtc acatcacgag atcctagtct 1320
ggttatcagc ttccacacta aaaattaggt cagaccaggc cccaaagtgc tctataaatt 1380
agaagctgga agatcctgaa atgaaactta agatttcaag gtcaaatatc tgcaactttg 1440
ttctcattac ctattgggcg cagcttctct ttaaaggctt gaattgagaa aagaggggtt 1500
ctgctgggtg gcaccttctt gctcttacct gctggtgcct tcctttccca ctacaggtaa 1560
agtccatggt tccctggccc gtgctggaaa agtgagaggt cagactccta aggtgagtga 1620
gagtattagt ggtcatggtg ttaggacttt ttttcctttc acagctaaac caagtccctg 1680
ggctcttact cggtttgcct tctccctccc tggagatgag cctgagggaa gggatgctag 1740
gtgtggaaga caggaaccag ggcctgatta accttccctt ctccaggtgg ccaaacagga 1800
gaagaagaag aagaagacag gtcgggctaa gcggcggatg cagtacaacc ggcgctttgt 1860
caacgttgtg cccacctttg gcaagaagaa gggccccaat gccaactctt aagtcttttg 1920
taattctggc tttctctaat aaaaaagcca cttagttcag tcatcgcatt gtttcatctt 1980
tacttgcaag gcctcaggga gaggtgtgct tctcgg 2016
//
Output file format
The output is a standard EMBOSS report file.
The results can be output in one of several styles by using the
command-line qualifier -rformat xxx, where 'xxx' is replaced by the
name of the required format. The available format names are: embl,
genbank, gff, pir, swiss, dasgff, debug, listfile, dbmotif, diffseq,
draw, restrict, excel, feattable, motif, nametable, regions, seqtable,
simple, srs, table, tagseq.
See: http://emboss.sf.net/docs/themes/ReportFormats.html for further
information on report formats.
tcode outputs a report format file. The default format is 'table'.
The resulting report file will be given a name relating to the analysed
sequence together with the .tcode suffix by default. Should there be no
sequence description, the default reverts to outfile.tcode.
tcode optionally outputs a graph to the specified graphics device.
The graphical display is output with the default file name tcode.1. and
then the name of the selected graphical display (e.g. png; ps).
The graph indicates the threshold for probably being coding with a
green horizontal line and the threshold for probably not being coding
with a red horizontal line.
Output files for usage example
File: x65921.tcode
########################################
# Program: tcode
# Rundate: Mon 15 Jul 2013 12:00:00
# Commandline: tcode
# -sequence tembl:x65921
# Report_format: table
# Report_file: x65921.tcode
########################################
#=======================================
#
# Sequence: X65921 from: 1 to: 2016
# HitCount: 606
#
# Fickett TESTCODE statistic
#
#=======================================
Start End Strand Score Estimation
1 200 + 0.617 Non-coding
4 203 + 0.586 Non-coding
7 206 + 0.617 Non-coding
10 209 + 0.729 Non-coding
13 212 + 0.696 Non-coding
16 215 + 0.734 Non-coding
19 218 + 0.779 No opinion
22 221 + 0.845 No opinion
25 224 + 0.889 No opinion
28 227 + 0.919 No opinion
31 230 + 0.831 No opinion
34 233 + 0.875 No opinion
37 236 + 0.970 Coding
40 239 + 1.122 Coding
43 242 + 1.110 Coding
46 245 + 1.002 Coding
49 248 + 0.979 Coding
52 251 + 1.076 Coding
55 254 + 0.966 Coding
58 257 + 0.931 No opinion
61 260 + 0.847 No opinion
64 263 + 0.847 No opinion
67 266 + 0.914 No opinion
70 269 + 0.951 Coding
73 272 + 1.031 Coding
76 275 + 0.870 No opinion
79 278 + 0.964 Coding
82 281 + 0.865 No opinion
85 284 + 1.040 Coding
88 287 + 0.924 No opinion
91 290 + 0.812 No opinion
[Part of this file has been deleted for brevity]
1696 1895 + 1.060 Coding
1699 1898 + 0.984 Coding
1702 1901 + 1.082 Coding
1705 1904 + 1.082 Coding
1708 1907 + 1.082 Coding
1711 1910 + 1.067 Coding
1714 1913 + 1.079 Coding
1717 1916 + 1.005 Coding
1720 1919 + 0.915 No opinion
1723 1922 + 0.954 Coding
1726 1925 + 0.872 No opinion
1729 1928 + 0.976 Coding
1732 1931 + 0.989 Coding
1735 1934 + 0.906 No opinion
1738 1937 + 0.832 No opinion
1741 1940 + 0.840 No opinion
1744 1943 + 0.840 No opinion
1747 1946 + 0.826 No opinion
1750 1949 + 0.858 No opinion
1753 1952 + 0.865 No opinion
1756 1955 + 0.878 No opinion
1759 1958 + 0.937 No opinion
1762 1961 + 1.012 Coding
1765 1964 + 0.968 Coding
1768 1967 + 0.979 Coding
1771 1970 + 0.979 Coding
1774 1973 + 0.937 No opinion
1777 1976 + 0.944 No opinion
1780 1979 + 0.944 No opinion
1783 1982 + 0.944 No opinion
1786 1985 + 0.890 No opinion
1789 1988 + 0.902 No opinion
1792 1991 + 0.851 No opinion
1795 1994 + 0.902 No opinion
1798 1997 + 0.902 No opinion
1801 2000 + 0.902 No opinion
1804 2003 + 0.821 No opinion
1807 2006 + 0.757 No opinion
1810 2009 + 0.730 Non-coding
1813 2012 + 0.708 Non-coding
1816 2015 + 0.708 Non-coding
#---------------------------------------
#---------------------------------------
#---------------------------------------
# Total_sequences: 1
# Total_length: 2016
# Reported_sequences: 1
# Reported_hitcount: 606
#---------------------------------------
Output files for usage example 2
Graphics File: tcode.ps
[tcode results]
Data files
EMBOSS data files are distributed with the application and stored in
the standard EMBOSS data directory, which is defined by the EMBOSS
environment variable EMBOSS_DATA.
To see the available EMBOSS data files, run:
% embossdata -showall
To fetch one of the data files (for example 'Exxx.dat') into your
current directory for you to inspect or modify, run:
% embossdata -fetch -file Exxx.dat
Users can provide their own data files in their own directories.
Project specific files can be put in the current directory, or for
tidier directory listings in a subdirectory called ".embossdata". Files
for all EMBOSS runs can be put in the user's home directory, or again
in a subdirectory called ".embossdata".
The directories are searched in the following order:
* . (your current directory)
* .embossdata (under your current directory)
* ~/ (your home directory)
* ~/.embossdata
The default data file (look-up table) is Etcode.dat which contains the
data from the original paper (1)
# Fickett TESTCODE data
# Nuc. Acids Res. 10(17) 5303-5318
#
# Position parameter values (last value must be 0.0)
1.9
1.8
1.7
1.6
1.5
1.4
1.3
1.2
1.1
0.0
#
#
# Content parameter values (last value must be 0.0)
0.33
0.31
0.29
0.27
0.25
0.23
0.21
0.17
0.00
#
#
# Position probabilities for A,C,G,T respectively
0.94 0.80 0.90 0.97
0.68 0.70 0.88 0.97
0.84 0.70 0.74 0.91
0.93 0.81 0.64 0.68
0.58 0.66 0.53 0.69
0.68 0.48 0.48 0.44
0.45 0.51 0.27 0.54
0.34 0.33 0.16 0.20
0.20 0.30 0.08 0.09
0.22 0.23 0.08 0.09
#
#
# Content probabilities for A,C,G,T respectively
0.28 0.82 0.40 0.28
0.49 0.64 0.54 0.24
0.44 0.51 0.47 0.39
0.55 0.64 0.64 0.40
0.62 0.59 0.64 0.55
0.49 0.59 0.73 0.75
0.67 0.43 0.41 0.56
0.65 0.44 0.41 0.69
0.81 0.39 0.33 0.51
0.21 0.31 0.29 0.58
#
#
# Weights for position
0.26
0.18
0.31
0.33
#
#
# Weights for content
0.11
0.12
0.15
0.14
This file is retrievable using EMBOSSDATA.
Window size is set by default to 200. The algorithm requires sufficient
sequence to perform the statistic on. The original paper suggests a
minimum window size of 200.
Window stepping increment is set by default to 3. This will ensure the
resulting information remains in frame.
Alternative Data Files
There are no alternative data files currently in the EMBOSS Data
directory, but alternative values may be user defined.
Notes
The TESTCODE statistic reflects the fact that codons are used with
unequal frequency and that oligonucleotides and nucleotides tend to be
repeated with a periodicity of three. The original paper reports that
the test had been thoroughly proven on 400,000 bases of sequence data:
it misclassifies 5% of the regions tested and gives an answer of "No
Opinion" one fifth of the time.
In the GCG package, the current (version 10.3) TESTCODE application's
apparent interpretation of the algorithm is: MAX(A1,A2,A3) /
MIN(A1,A2,A3) The EMBOSS tcode program uses the correct Fickett
algorithm equation: MAX(A1,A2,A3) / MIN(A1,A2,A3) + 1 thus any plot
using the GCG TESTCODE aplication will be slightly higher than the
tcode equivalent.
References
1. Fickett, J.W. (1982) Nucleic Acids Research 10(17) pp.5303-5318
"Recognition of protein coding regions in DNA sequences"
Warnings
The program will ignore ambiguity codes in the nucleic acid sequence
and just accept the four common bases. This is a function of the
algorithm, and the data tables.
Diagnostic Error Messages
Standard error messages are given for incorrect sequence input.
Exit status
It always exits with status 0.
See also
Program name Description
checktrans Report STOP codons and ORF statistics of a protein
getorf Find and extract open reading frames (ORFs)
marscan Find matrix/scaffold recognition (MRS) signatures in DNA
sequences
plotorf Plot potential open reading frames in a nucleotide sequence
showorf Display a nucleotide sequence and translation in pretty format
sixpack Display a DNA sequence with 6-frame translation and ORFs
syco Draw synonymous codon usage statistic plot for a nucleotide
sequence
wobble Plot third base position variability in a nucleotide sequence
See Elsewhere
TESTCODE - GCG package, Accelrys Inc. Uses a different interpretation
of the same algorithm. Source code unavailable.
SPIN - "Uneven positional base preferences" Staden software. Free to
academics, versions for both X and Windows platforms.
Author(s)
Alan Bleasby
European Bioinformatics Institute, Wellcome Trust Genome Campus,
Hinxton, Cambridge CB10 1SD, UK
Please report all bugs to the EMBOSS bug team
(emboss-bug (c) emboss.open-bio.org) not to the original author.
History
Date of original completion: 2nd March 2003
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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