tcode.txt

emboss的linux版本的源代码

     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: hsfau1.tcode

########################################
# Program: tcode
# Rundate: Sat 15 Jul 2006 12:00:00
# Commandline: tcode
#    -sequence tembl:hsfau1
# Report_format: table
# Report_file: hsfau1.tcode
########################################

#=======================================
#
# Sequence: HSFAU1     from: 1   to: 2016
# HitCount: 606
#
# Fickett TESTCODE statistic
#
#=======================================

  Start     End   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]

  File: hsfau1.tcode

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

   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

   None.

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 MAR/SAR sites in nucleic sequences
   plotorf      Plot potential open reading frames
   showorf      Pretty output of DNA translations
   sixpack      Display a DNA sequence with 6-frame translation and ORFs
   syco         Synonymous codon usage Gribskov statistic plot
   wobble       Wobble base plot

  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