                                    cusp



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Function

   Create a codon usage table from nucleotide sequence(s)

Description

   cusp calculates a codon usage table for one or more nucleotide coding
   sequences and writes the table to file.

   The codon usage table gives for each codon: i. Sequence of the codon.
   ii. The encoded amino acid. iii. The proportion of usage of the codon
   among its redundant set, i.e. the set of codons which code for this
   codon's amino acid. iv. The expected number of codons, given the input
   sequence(s), per 1000 bases. v. The observed number of codons in the
   input sequences.

Usage

   Here is a sample session with cusp

   This example uses only one input sequence. The normal use would be to
   use a set of coding sequences as the input.


% cusp -sbeg 135 -send 1292
Create a codon usage table from nucleotide sequence(s)
Input nucleotide sequence(s): tembl:x13776
Output file [x13776.cusp]:


   Go to the input files for this example
   Go to the output files for this example

Command line arguments

Create a codon usage table from nucleotide sequence(s)
Version: EMBOSS:6.5.6.0

   Standard (Mandatory) qualifiers:
  [-sequence]          seqall     Nucleotide sequence(s) filename and optional
                                  format, or reference (input USA)
  [-outfile]           outfile    [*.cusp] Output file name

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers: (none)
   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
   -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
   -odirectory2        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

  Input files for usage example

   'tembl:x13776' is a sequence entry in the example nucleic acid database
   'tembl'

  Database entry: tembl:x13776

ID   X13776; SV 1; linear; genomic DNA; STD; PRO; 2167 BP.
XX
AC   X13776; M43175;
XX
DT   19-APR-1989 (Rel. 19, Created)
DT   14-NOV-2006 (Rel. 89, Last updated, Version 24)
XX
DE   Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase regulation
XX
KW   aliphatic amidase regulator; amiC gene; amiR gene.
XX
OS   Pseudomonas aeruginosa
OC   Bacteria; Proteobacteria; Gammaproteobacteria; Pseudomonadales;
OC   Pseudomonadaceae; Pseudomonas.
XX
RN   [1]
RP   1167-2167
RA   Rice P.M.;
RT   ;
RL   Submitted (16-DEC-1988) to the INSDC.
RL   Rice P.M., EMBL, Postfach 10-2209, Meyerhofstrasse 1, 6900 Heidelberg, FRG.
XX
RN   [2]
RP   1167-2167
RX   DOI; 10.1016/0014-5793(89)80249-2.
RX   PUBMED; 2495988.
RA   Lowe N., Rice P.M., Drew R.E.;
RT   "Nucleotide sequence of the aliphatic amidase regulator gene (amiR) of
RT   Pseudomonas aeruginosa";
RL   FEBS Lett. 246(1-2):39-43(1989).
XX
RN   [3]
RP   1-1292
RX   PUBMED; 1907262.
RA   Wilson S., Drew R.;
RT   "Cloning and DNA sequence of amiC, a new gene regulating expression of the
RT   Pseudomonas aeruginosa aliphatic amidase, and purification of the amiC
RT   product";
RL   J. Bacteriol. 173(16):4914-4921(1991).
XX
RN   [4]
RP   1-2167
RA   Rice P.M.;
RT   ;
RL   Submitted (04-SEP-1991) to the INSDC.
RL   Rice P.M., EMBL, Postfach 10-2209, Meyerhofstrasse 1, 6900 Heidelberg, FRG.
XX
DR   GOA; Q51417.
DR   InterPro; IPR003211; AmiSUreI_transpt.
DR   UniProtKB/Swiss-Prot; Q51417; AMIS_PSEAE.


  [Part of this file has been deleted for brevity]

FT                   /note="ClaI fragment deleted in pSW36,  constitutive
FT                   phenotype"
FT   misc_feature    1
FT                   /note="last base of an XhoI site"
FT   misc_feature    648..653
FT                   /note="end of 658bp XhoI fragment, deletion in  pSW3 causes
FT                   constitutive expression of amiE"
FT   misc_difference 1281
FT                   /replace="g"
FT                   /note="conflict"
FT                   /citation=[3]
XX
SQ   Sequence 2167 BP; 363 A; 712 C; 730 G; 362 T; 0 other;
     ggtaccgctg gccgagcatc tgctcgatca ccaccagccg ggcgacggga actgcacgat        60
     ctacctggcg agcctggagc acgagcgggt tcgcttcgta cggcgctgag cgacagtcac       120
     aggagaggaa acggatggga tcgcaccagg agcggccgct gatcggcctg ctgttctccg       180
     aaaccggcgt caccgccgat atcgagcgct cgcacgcgta tggcgcattg ctcgcggtcg       240
     agcaactgaa ccgcgagggc ggcgtcggcg gtcgcccgat cgaaacgctg tcccaggacc       300
     ccggcggcga cccggaccgc tatcggctgt gcgccgagga cttcattcgc aaccgggggg       360
     tacggttcct cgtgggctgc tacatgtcgc acacgcgcaa ggcggtgatg ccggtggtcg       420
     agcgcgccga cgcgctgctc tgctacccga ccccctacga gggcttcgag tattcgccga       480
     acatcgtcta cggcggtccg gcgccgaacc agaacagtgc gccgctggcg gcgtacctga       540
     ttcgccacta cggcgagcgg gtggtgttca tcggctcgga ctacatctat ccgcgggaaa       600
     gcaaccatgt gatgcgccac ctgtatcgcc agcacggcgg cacggtgctc gaggaaatct       660
     acattccgct gtatccctcc gacgacgact tgcagcgcgc cgtcgagcgc atctaccagg       720
     cgcgcgccga cgtggtcttc tccaccgtgg tgggcaccgg caccgccgag ctgtatcgcg       780
     ccatcgcccg tcgctacggc gacggcaggc ggccgccgat cgccagcctg accaccagcg       840
     aggcggaggt ggcgaagatg gagagtgacg tggcagaggg gcaggtggtg gtcgcgcctt       900
     acttctccag catcgatacg cccgccagcc gggccttcgt ccaggcctgc catggtttct       960
     tcccggagaa cgcgaccatc accgcctggg ccgaggcggc ctactggcag accttgttgc      1020
     tcggccgcgc cgcgcaggcc gcaggcaact ggcgggtgga agacgtgcag cggcacctgt      1080
     acgacatcga catcgacgcg ccacaggggc cggtccgggt ggagcgccag aacaaccaca      1140
     gccgcctgtc ttcgcgcatc gcggaaatcg atgcgcgcgg cgtgttccag gtccgctggc      1200
     agtcgcccga accgattcgc cccgaccctt atgtcgtcgt gcataacctc gacgactggt      1260
     ccgccagcat gggcggggga ccgctcccat gagcgccaac tcgctgctcg gcagcctgcg      1320
     cgagttgcag gtgctggtcc tcaacccgcc gggggaggtc agcgacgccc tggtcttgca      1380
     gctgatccgc atcggttgtt cggtgcgcca gtgctggccg ccgccggaag ccttcgacgt      1440
     gccggtggac gtggtcttca ccagcatttt ccagaatggc caccacgacg agatcgctgc      1500
     gctgctcgcc gccgggactc cgcgcactac cctggtggcg ctggtggagt acgaaagccc      1560
     cgcggtgctc tcgcagatca tcgagctgga gtgccacggc gtgatcaccc agccgctcga      1620
     tgcccaccgg gtgctgcctg tgctggtatc ggcgcggcgc atcagcgagg aaatggcgaa      1680
     gctgaagcag aagaccgagc agctccagga ccgcatcgcc ggccaggccc ggatcaacca      1740
     ggccaaggtg ttgctgatgc agcgccatgg ctgggacgag cgcgaggcgc accagcacct      1800
     gtcgcgggaa gcgatgaagc ggcgcgagcc gatcctgaag atcgctcagg agttgctggg      1860
     aaacgagccg tccgcctgag cgatccgggc cgaccagaac aataacaaga ggggtatcgt      1920
     catcatgctg ggactggttc tgctgtacgt tggcgcggtg ctgtttctca atgccgtctg      1980
     gttgctgggc aagatcagcg gtcgggaggt ggcggtgatc aacttcctgg tcggcgtgct      2040
     gagcgcctgc gtcgcgttct acctgatctt ttccgcagca gccgggcagg gctcgctgaa      2100
     ggccggagcg ctgaccctgc tattcgcttt tacctatctg tgggtggccg ccaaccagtt      2160
     cctcgag                                                                2167
//

Output file format

  Output files for usage example

  File: x13776.cusp

#CdsCount: 1

#Coding GC 67.79%
#1st letter GC 67.88%
#2nd letter GC 46.89%
#3rd letter GC 88.60%

#Codon AA Fraction Frequency Number
GCA    A     0.077     7.772      3
GCC    A     0.462    46.632     18
GCG    A     0.462    46.632     18
GCT    A     0.000     0.000      0
TGC    C     1.000    10.363      4
TGT    C     0.000     0.000      0
GAC    D     0.864    49.223     19
GAT    D     0.136     7.772      3
GAA    E     0.269    18.135      7
GAG    E     0.731    49.223     19
TTC    F     1.000    28.497     11
TTT    F     0.000     0.000      0
GGA    G     0.062     5.181      2
GGC    G     0.719    59.585     23
GGG    G     0.125    10.363      4
GGT    G     0.094     7.772      3
CAC    H     0.727    20.725      8
CAT    H     0.273     7.772      3
ATA    I     0.000     0.000      0
ATC    I     0.800    41.451     16
ATT    I     0.200    10.363      4
AAA    K     0.000     0.000      0
AAG    K     1.000     5.181      2
CTA    L     0.000     0.000      0
CTC    L     0.269    18.135      7
CTG    L     0.577    38.860     15
CTT    L     0.000     0.000      0
TTA    L     0.000     0.000      0
TTG    L     0.154    10.363      4
ATG    M     1.000    15.544      6
AAC    N     1.000    28.497     11
AAT    N     0.000     0.000      0
CCA    P     0.074     5.181      2
CCC    P     0.222    15.544      6
CCG    P     0.630    44.041     17
CCT    P     0.074     5.181      2
CAA    Q     0.062     2.591      1
CAG    Q     0.938    38.860     15
AGA    R     0.000     0.000      0
AGG    R     0.029     2.591      1
CGA    R     0.000     0.000      0
CGC    R     0.629    56.995     22
CGG    R     0.314    28.497     11
CGT    R     0.029     2.591      1
AGC    S     0.304    18.135      7
AGT    S     0.087     5.181      2
TCA    S     0.000     0.000      0
TCC    S     0.261    15.544      6
TCG    S     0.304    18.135      7
TCT    S     0.043     2.591      1
ACA    T     0.000     0.000      0
ACC    T     0.733    28.497     11
ACG    T     0.267    10.363      4
ACT    T     0.000     0.000      0
GTA    V     0.030     2.591      1
GTC    V     0.394    33.679     13
GTG    V     0.576    49.223     19
GTT    V     0.000     0.000      0
TGG    W     1.000    12.953      5
TAC    Y     0.619    33.679     13
TAT    Y     0.381    20.725      8
TAA    *     0.000     0.000      0
TAG    *     0.000     0.000      0
TGA    *     1.000     2.591      1

   The example shown reads a single CDS from Pseudomonas aeruginosa which
   has a very high GC content and a strong coding bias, as shown by the
   codons for Alanine where those ending with G or C are used almost
   exclusively.

   The columns are as follows: i. "Codon" (sequence of the codon). ii.
   "AA" (the encoded amino acid). iii. "Fraction" (the proportion of usage
   of the codon among its redundant set, i.e. the set of codons which code
   for this codon's amino acid). iv. "Frequency" (the expected number of
   codons, given the input sequence(s), per 1000 bases). This will be an
   extrapolation if the sequence is shorter than 1000 bases. v. "Number"
   (the observed number of codons in the input sequences).

   If multiple sequences are input then the statistics are given for all
   of the sequences together, not individually.

Data files

   cusp reads a codon usage file as a template for it's output file. The
   data in this table is ignored entirely. This functionality is
   hard-coded and invisible to the user.

   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

Notes

   None.

References

   None.

Warnings

   None.

Diagnostic Error Messages

   None.

Exit status

   Always exits with status 0.

Known bugs

   None.

See also

   Program name     Description
   cai              Calculate codon adaptation index
   chips            Calculate Nc codon usage statistic
   codcmp           Codon usage table comparison
   codcopy          Copy and reformat a codon usage table
   syco             Draw synonymous codon usage statistic plot for a nucleotide
                    sequence

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

Target users

   This program is intended to be used by everyone and everything, from
   naive users to embedded scripts.

Comments

   None
