
                                   tcode 



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

   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
*  -graph              xygraph    [$EMBOSS_GRAPHICS value, or x11] Graph type
                                  (ps, hpgl, hp7470, hp7580, meta, cps, x11,
                                  tekt, tek, none, data, xterm, png, gif)

   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
   -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

   "-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. 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

   tcode reads any normal sequence USAs.

   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 EMBL/GenBank/DDBJ databases.
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   GDB; 191789.
DR   GDB; 191790.
DR   GDB; 354872.
DR   GDB; 4590236.
XX
FH   Key             Location/Qualifiers
FH
FT   source          1..2016
FT                   /organism="Homo sapiens"
FT                   /mol_type="genomic DNA"
FT                   /clone_lib="CML cosmid"
FT                   /clone="15.1"
FT                   /db_xref="taxon:9606"
FT   mRNA            join(408..504,774..856,951..1095,1557..1612,1787..>1912)
FT                   /gene="fau 1"
FT   exon            408..504
FT                   /number=1


  [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        6
0
     ggcaaaacta aggccccaag taggaatgcc ttagttttcg gggttaacaa tgattaacac       12
0
     tgagcctcac acccacgcga tgccctcagc tcctcgctca gcgctctcac caacagccgt       18
0
     agcccgcagc cccgctggac accggttctc catccccgca gcgtagcccg gaacatggta       24
0
     gctgccatct ttacctgcta cgccagcctt ctgtgcgcgc aactgtctgg tcccgccccg       30
0
     tcctgcgcga gctgctgccc aggcaggttc gccggtgcga gcgtaaaggg gcggagctag       36
0
     gactgccttg ggcggtacaa atagcaggga accgcgcggt cgctcagcag tgacgtgaca       42
0
     cgcagcccac ggtctgtact gacgcgccct cgcttcttcc tctttctcga ctccatcttc       48
0
     gcggtagctg ggaccgccgt tcaggtaaga atggggcctt ggctggatcc gaagggcttg       54
0
     tagcaggttg gctgcggggt cagaaggcgc ggggggaacc gaagaacggg gcctgctccg       60
0
     tggccctgct ccagtcccta tccgaactcc ttgggaggca ctggccttcc gcacgtgagc       66
0
     cgccgcgacc accatcccgt cgcgatcgtt tctggaccgc tttccactcc caaatctcct       72
0
     ttatcccaga gcatttcttg gcttctctta caagccgtct tttctttact cagtcgccaa       78
0
     tatgcagctc tttgtccgcg cccaggagct acacaccttc gaggtgaccg gccaggaaac       84
0
     ggtcgcccag atcaaggtaa ggctgcttgg tgcgccctgg gttccatttt cttgtgctct       90
0
     tcactctcgc ggcccgaggg aacgcttacg agccttatct ttccctgtag gctcatgtag       96
0
     cctcactgga gggcattgcc ccggaagatc aagtcgtgct cctggcaggc gcgcccctgg      102
0
     aggatgaggc cactctgggc cagtgcgggg tggaggccct gactaccctg gaagtagcag      108
0
     gccgcatgct tggaggtgag tgagagagga atgttctttg aagtaccggt aagcgtctag      114
0
     tgagtgtggg gtgcatagtc ctgacagctg agtgtcacac ctatggtaat agagtacttc      120
0
     tcactgtctt cagttcagag tgattcttcc tgtttacatc cctcatgttg aacacagacg      126
0
     tccatgggag actgagccag agtgtagttg tatttcagtc acatcacgag atcctagtct      132
0
     ggttatcagc ttccacacta aaaattaggt cagaccaggc cccaaagtgc tctataaatt      138
0
     agaagctgga agatcctgaa atgaaactta agatttcaag gtcaaatatc tgcaactttg      144
0
     ttctcattac ctattgggcg cagcttctct ttaaaggctt gaattgagaa aagaggggtt      150
0
     ctgctgggtg gcaccttctt gctcttacct gctggtgcct tcctttccca ctacaggtaa      156
0
     agtccatggt tccctggccc gtgctggaaa agtgagaggt cagactccta aggtgagtga      162
0
     gagtattagt ggtcatggtg ttaggacttt ttttcctttc acagctaaac caagtccctg      168
0
     ggctcttact cggtttgcct tctccctccc tggagatgag cctgagggaa gggatgctag      174
0
     gtgtggaaga caggaaccag ggcctgatta accttccctt ctccaggtgg ccaaacagga      180
0
     gaagaagaag aagaagacag gtcgggctaa gcggcggatg cagtacaacc ggcgctttgt      186
0
     caacgttgtg cccacctttg gcaagaagaa gggccccaat gccaactctt aagtcttttg      192
0
     taattctggc tttctctaat aaaaaagcca cttagttcag tcatcgcatt gtttcatctt      198
0
     tacttgcaag gcctcaggga gaggtgtgct tctcgg                                201
6
//

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, trace, listfile, dbmotif, diffseq, excel,
   feattable, motif, 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: Tue 15 Jul 2008 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       +   0.673 Non-coding
      4     203       +   0.681 Non-coding
      7     206       +   0.649 Non-coding
     10     209       +   0.649 Non-coding
     13     212       +   0.649 Non-coding
     16     215       +   0.657 Non-coding
     19     218       +   0.687 Non-coding
     22     221       +   0.767 No opinion
     25     224       +   0.800 No opinion
     28     227       +   0.782 No opinion
     31     230       +   0.779 No opinion
     34     233       +   0.839 No opinion
     37     236       +   0.951 Coding
     40     239       +   0.916 No opinion
     43     242       +   0.900 No opinion
     46     245       +   0.839 No opinion
     49     248       +   0.835 No opinion
     52     251       +   0.926 No opinion
     55     254       +   0.887 No opinion
     58     257       +   0.927 No opinion
     61     260       +   0.873 No opinion
     64     263       +   0.873 No opinion
     67     266       +   0.927 No opinion
     70     269       +   1.033 Coding
     73     272       +   1.044 Coding
     76     275       +   1.012 Coding
     79     278       +   1.105 Coding
     82     281       +   1.022 Coding
     85     284       +   1.098 Coding
     88     287       +   0.976 Coding
     91     290       +   0.962 Coding


  [Part of this file has been deleted for brevity]

   1690    1889       +   0.907 No opinion
   1693    1892       +   1.005 Coding
   1696    1895       +   0.985 Coding
   1699    1898       +   0.907 No opinion
   1702    1901       +   0.985 Coding
   1705    1904       +   0.985 Coding
   1708    1907       +   0.988 Coding
   1711    1910       +   0.981 Coding
   1714    1913       +   1.001 Coding
   1717    1916       +   1.001 Coding
   1720    1919       +   1.004 Coding
   1723    1922       +   0.975 Coding
   1726    1925       +   0.975 Coding
   1729    1928       +   0.927 No opinion
   1732    1931       +   0.939 No opinion
   1735    1934       +   0.930 No opinion
   1738    1937       +   0.860 No opinion
   1741    1940       +   0.876 No opinion
   1744    1943       +   0.876 No opinion
   1747    1946       +   0.836 No opinion
   1750    1949       +   0.883 No opinion
   1753    1952       +   0.934 No opinion
   1756    1955       +   0.965 Coding
   1759    1958       +   1.012 Coding
   1762    1961       +   1.025 Coding
   1765    1964       +   0.940 No opinion
   1768    1967       +   0.978 Coding
   1771    1970       +   0.978 Coding
   1774    1973       +   1.012 Coding
   1777    1976       +   1.023 Coding
   1780    1979       +   1.023 Coding
   1783    1982       +   1.023 Coding
   1786    1985       +   1.012 Coding
   1789    1988       +   0.972 Coding
   1792    1991       +   0.943 No opinion
   1795    1994       +   1.031 Coding
   1798    1997       +   1.031 Coding
   1801    2000       +   0.926 No opinion
   1804    2003       +   0.845 No opinion
   1807    2006       +   0.804 No opinion
   1810    2009       +   0.765 No opinion
   1813    2012       +   0.765 No opinion
   1816    2015       +   0.765 No opinion

#---------------------------------------
#---------------------------------------

#---------------------------------------
# Total_sequences: 1
# Total_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
   getorf Finds and extracts open reading frames (ORFs)
   marscan Finds 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 statictic 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 (ajb © ebi.ac.uk)
   European Bioinformatics Institute, Wellcome Trust Genome Campus,
   Hinxton, Cambridge CB10 1SD, UK

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
