tcode

Wiki

The master copies of EMBOSS documentation are available at http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki.

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]: ```

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 ```

Command line arguments

 ```Identify protein-coding regions using Fickett TESTCODE statistic Version: EMBOSS:6.4.0.0 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 -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 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 ```

Qualifier Type Description Allowed values Default
Standard (Mandatory) qualifiers
[-sequence]
(Parameter 1)
seqall Nucleotide sequence(s) filename and optional format, or reference (input USA) Readable sequence(s) Required
-window integer 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 200
-outfile report Output report file name (default -rformat table) <*>.tcode
-graph xygraph Graph type EMBOSS has a list of known devices, including ps, hpgl, hp7470, hp7580, meta, cps, x11, tek, tekt, none, data, xterm, png, gif, pdf, svg EMBOSS_GRAPHICS value, or x11
(none)
-datafile datafile The default data file is Etcode.dat and contains coding probabilities for each base. The probabilities are for both positional and compositional information. Data file Etcode.dat
-step integer 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 3
-plot toggle 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. Toggle value Yes/No No
Associated qualifiers
"-sequence" associated seqall qualifiers
-sbegin1
-sbegin_sequence
integer Start of each sequence to be used Any integer value 0
-send1
-send_sequence
integer End of each sequence to be used Any integer value 0
-sreverse1
-sreverse_sequence
boolean Reverse (if DNA) Boolean value Yes/No N
boolean Ask for begin/end/reverse Boolean value Yes/No N
-snucleotide1
-snucleotide_sequence
boolean Sequence is nucleotide Boolean value Yes/No N
-sprotein1
-sprotein_sequence
boolean Sequence is protein Boolean value Yes/No N
-slower1
-slower_sequence
boolean Make lower case Boolean value Yes/No N
-supper1
-supper_sequence
boolean Make upper case Boolean value Yes/No N
-sformat1
-sformat_sequence
string Input sequence format Any string
-sdbname1
-sdbname_sequence
string Database name Any string
-sid1
-sid_sequence
string Entryname Any string
-ufo1
-ufo_sequence
string UFO features Any string
-fformat1
-fformat_sequence
string Features format Any string
-fopenfile1
-fopenfile_sequence
string Features file name Any string
"-outfile" associated report qualifiers
-rformat string Report format Any string table
-rname string Base file name Any string
-rextension string File name extension Any string
-rdirectory string Output directory Any string
-raccshow boolean Show accession number in the report Boolean value Yes/No N
-rdesshow boolean Show description in the report Boolean value Yes/No N
-rscoreshow boolean Show the score in the report Boolean value Yes/No Y
-rstrandshow boolean Show the nucleotide strand in the report Boolean value Yes/No Y
-rusashow boolean Show the full USA in the report Boolean value Yes/No N
-rmaxall integer Maximum total hits to report Any integer value 0
-rmaxseq integer Maximum hits to report for one sequence Any integer value 0
"-graph" associated xygraph qualifiers
-gprompt boolean Graph prompting Boolean value Yes/No N
-gdesc string Graph description Any string Fickett testcode plot
-gtitle string Graph title Any string
-gsubtitle string Graph subtitle Any string
-gxtitle string Graph x axis title Any string
-gytitle string Graph y axis title Any string
-goutfile string Output file for non interactive displays Any string
-gdirectory string Output directory Any string
General qualifiers
-auto boolean Turn off prompts Boolean value Yes/No N
-stdout boolean Write first file to standard output Boolean value Yes/No N
-filter boolean Read first file from standard input, write first file to standard output Boolean value Yes/No N
-options boolean Prompt for standard and additional values Boolean value Yes/No N
-debug boolean Write debug output to program.dbg Boolean value Yes/No N
-verbose boolean Report some/full command line options Boolean value Yes/No Y
-help boolean Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose Boolean value Yes/No N
-warning boolean Report warnings Boolean value Yes/No Y
-fatal boolean Report fatal errors Boolean value Yes/No Y
-die boolean Report dying program messages Boolean value Yes/No Y
-version boolean Report version number and exit Boolean value Yes/No N

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 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 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.

File: x65921.tcode

 ```######################################## # Program: tcode # Rundate: Fri 15 Jul 2011 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 + 0.692 Non-coding 4 203 + 0.666 Non-coding 7 206 + 0.692 Non-coding 10 209 + 0.797 No opinion 13 212 + 0.766 No opinion 16 215 + 0.805 No opinion 19 218 + 0.824 No opinion 22 221 + 0.901 No opinion 25 224 + 0.934 No opinion 28 227 + 0.977 Coding 31 230 + 0.903 No opinion 34 233 + 0.942 No opinion 37 236 + 1.043 Coding 40 239 + 1.179 Coding 43 242 + 1.149 Coding 46 245 + 1.031 Coding 49 248 + 1.012 Coding 52 251 + 1.121 Coding 55 254 + 1.004 Coding 58 257 + 0.970 Coding 61 260 + 0.941 No opinion 64 263 + 0.941 No opinion 67 266 + 0.995 Coding 70 269 + 1.029 Coding 73 272 + 1.072 Coding 76 275 + 0.930 No opinion 79 278 + 1.023 Coding 82 281 + 0.959 Coding 85 284 + 1.107 Coding 88 287 + 0.985 Coding 91 290 + 0.880 No opinion [Part of this file has been deleted for brevity] 1696 1895 + 1.099 Coding 1699 1898 + 1.027 Coding 1702 1901 + 1.067 Coding 1705 1904 + 1.067 Coding 1708 1907 + 1.067 Coding 1711 1910 + 1.086 Coding 1714 1913 + 1.024 Coding 1717 1916 + 1.016 Coding 1720 1919 + 0.933 No opinion 1723 1922 + 0.964 Coding 1726 1925 + 0.887 No opinion 1729 1928 + 0.973 Coding 1732 1931 + 0.991 Coding 1735 1934 + 0.928 No opinion 1738 1937 + 0.862 No opinion 1741 1940 + 0.848 No opinion 1744 1943 + 0.848 No opinion 1747 1946 + 0.797 No opinion 1750 1949 + 0.844 No opinion 1753 1952 + 0.873 No opinion 1756 1955 + 0.883 No opinion 1759 1958 + 0.959 Coding 1762 1961 + 1.002 Coding 1765 1964 + 0.977 Coding 1768 1967 + 0.955 Coding 1771 1970 + 0.955 Coding 1774 1973 + 0.959 Coding 1777 1976 + 0.969 Coding 1780 1979 + 0.969 Coding 1783 1982 + 0.969 Coding 1786 1985 + 0.911 No opinion 1789 1988 + 0.948 No opinion 1792 1991 + 0.865 No opinion 1795 1994 + 0.948 No opinion 1798 1997 + 0.948 No opinion 1801 2000 + 0.948 No opinion 1804 2003 + 0.901 No opinion 1807 2006 + 0.879 No opinion 1810 2009 + 0.840 No opinion 1813 2012 + 0.785 No opinion 1816 2015 + 0.785 No opinion #--------------------------------------- #--------------------------------------- #--------------------------------------- # Total_sequences: 1 # Total_length: 2016 # Reported_sequences: 1 # Reported_hitcount: 606 #--------------------------------------- ```

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:

• .embossdata (under your current 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.

Program name Description
checktrans Reports STOP codons and ORF statistics of a protein
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 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 © 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.