                                   complex



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Function

   Find the linguistic complexity in nucleotide sequences

Description

Usage

   Here is a sample session with complex


% complex -omnia
Find the linguistic complexity in nucleotide sequences
Input nucleotide sequence(s): tembl:x*
Window length [100]:
Step size [5]:
Minimum word length [4]:
Maximum word length [6]:
Program complex output file [x59796.complex]:
output sequence(s) [x59796.fasta]:


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

Command line arguments

Find the linguistic complexity in nucleotide sequences
Version: EMBOSS:6.3.1

   Standard (Mandatory) qualifiers (* if not always prompted):
  [-sequence]          seqall     Nucleotide sequence(s) filename and optional
                                  format, or reference (input USA)
   -lwin               integer    [100] Window length (Integer 1 or more)
   -step               integer    [5] Displacement of the window over the
                                  sequence (Integer 1 or more)
   -jmin               integer    [4] Minimum word length (Integer from 2 to
                                  20)
   -jmax               integer    [6] Maximum word length (Integer from 2 to
                                  50)
  [-outfile]           outfile    [*.complex] Program complex output file
*  -outseq             seqoutall  [.] Sequence set(s)
                                  filename and optional format (output USA)

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers:
   -omnia              toggle     [N] Calculate over a set of sequences
   -sim                integer    [0] Calculate the linguistic complexity by
                                  comparison with a number of simulations
                                  having a uniform distribution of bases (Any
                                  integer value)
   -freq               boolean    [N] Execute the simulation of a sequence
                                  based on the base frequency of the original
                                  sequence
   -print              boolean    [N] Generate a file named UjTable containing
                                  the values of Uj for each word j in the
                                  real sequence(s) and in any simulated
                                  sequences
   -ujtablefile        outfile    [complex.ujtable] Program complex temporary
                                  output file

   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
   -odirectory2        string     Output directory

   "-ujtablefile" associated qualifiers
   -odirectory         string     Output directory

   "-outseq" associated qualifiers
   -osformat           string     Output seq format
   -osextension        string     File name extension
   -osname             string     Base file name
   -osdirectory        string     Output directory
   -osdbname           string     Database name to add
   -ossingle           boolean    Separate file for each entry
   -oufo               string     UFO features
   -offormat           string     Features format
   -ofname             string     Features file name
   -ofdirectory        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:x*' is a sequence entry in the example nucleic acid database
   'tembl'

Output file format

   Sequence TEMBL:HHTETRA contains repeats and is included in the test
   database for repeat analysis.

  Output files for usage example

  File: complex.ujtable


  File: x59796.complex

Length of window : 100
jmin : 4
jmax : 6
step : 5
Execution without simulation
----------------------------------------------------------------------------
|                  |                  |                  |                  |
|     number of    |      name of     |     length of    |      value of    |
|     sequence     |     sequence     |     sequence     |     complexity   |
|                  |                  |                  |                  |
----------------------------------------------------------------------------
         1                      X59796           3170             0.6921
         2                      X65923            518             0.6739
         3                      X65921           2016             0.7105
         4                      X51466           3075             0.6925
         5                      X07523           1658             0.7314
         6                      X03487            512             0.5609
         7                      X03488           1132             0.7217
         8                      X07797           1675             0.6201
         9                      X51872           1832             0.6916
        10                      X77160           1212             0.6596
        11                      X13776           2167             0.6562
        12                      X77161           1130             0.6989

  File: x59796.fasta

>X59796 X59796.1 H.sapiens mRNA for cadherin-5
ctccactcacgctcagccctggacggacaggcagtccaacggaacagaaacatccctcag
cccacaggcacgatctgttcctcctgggaagatgcagaggctcatgatgctcctcgccac
atcgggcgcctgcctgggcctgctggcagtggcagcagtggcagcagcaggtgctaaccc
tgcccaacgggacacccacagcctgctgcccacccaccggcgccaaaagagagattggat
ttggaaccagatgcacattgatgaagagaaaaacacctcacttccccatcatgtaggcaa
gatcaagtcaagcgtgagtcgcaagaatgccaagtacctgctcaaaggagaatatgtggg
caaggtcttccgggtcgatgcagagacaggagacgtgttcgccattgagaggctggaccg
ggagaatatctcagagtaccacctcactgctgtcattgtggacaaggacactggcgaaaa
cctggagactccttccagcttcaccatcaaagttcatgacgtgaacgacaactggcctgt
gttcacgcatcggttgttcaatgcgtccgtgcctgagtcgtcggctgtggggacctcagt
catctctgtgacagcagtggatgcagacgaccccactgtgggagaccacgcctctgtcat
gtaccaaatcctgaaggggaaagagtattttgccatcgataattctggacgtattatcac
aataacgaaaagcttggaccgagagaagcaggccaggtatgagatcgtggtggaagcgcg
agatgcccagggcctccggggggactcgggcacggccaccgtgctggtcactctgcaaga
catcaatgacaacttccccttcttcacccagaccaagtacacatttgtcgtgcctgaaga
cacccgtgtgggcacctctgtgggctctctgtttgttgaggacccagatgagccccagaa
ccggatgaccaagtacagcatcttgcggggcgactaccaggacgctttcaccattgagac
aaaccccgcccacaacgagggcatcatcaagcccatgaagcctctggattatgaatacat
ccagcaatacagcttcatagtcgaggccacagaccccaccatcgacctccgatacatgag
ccctcccgcgggaaacagagcccaggtcattatcaacatcacagatgtggacgagccccc
cattttccagcagcctttctaccacttccagctgaaggaaaaccagaagaagcctctgat
tggcacagtgctggccatggaccctgatgcggctaggcatagcattggatactccatccg
caggaccagtgacaagggccagttcttccgagtcacaaaaaagggggacatttacaatga
gaaagaactggacagagaagtctacccctggtataacctgactgtggaggccaaagaact
ggattccactggaacccccacaggaaaagaatccattgtgcaagtccacattgaagtttt
ggatgagaatgacaatgccccggagtttgccaagccctaccagcccaaagtgtgtgagaa
cgctgtccatggccagctggtcctgcagatctccgcaatagacaaggacataacaccacg
aaacgtgaagttcaaattcatcttgaatactgagaacaactttaccctcacggataatca
cgataacacggccaacatcacagtcaagtatgggcagtttgaccgggagcataccaaggt
ccacttcctacccgtggtcatctcagacaatgggatgccaagtcgcacgggcaccagcac
gctgaccgtggccgtgtgcaagtgcaacgagcagggcgagttcaccttctgcgaggatat
ggccgcccaggtgggcgtgagcatccaggcagtggtagccatcttactctgcatcctcac
catcacagtgatcaccctgctcatcttcctgcggcggcggctccggaagcaggcccgcgc
gcacggcaagagcgtgccggagatccacgagcagctggtcacctacgacgaggagggcgg
cggcgagatggacaccaccagctacgatgtgtcggtgctcaactcggtgcgccgcggcgg
ggccaagcccccgcggcccgcgctggacgcccggccttccctctatgcgcaggtgcagaa
gccaccgaggcacgcgcctggggcacacggagggcccggggagatggcagccatgatcga
ggtgaagaaggacgaggcggaccacgacggcgacggccccccctacgacacgctgcacat
ctacggctacgagggctccgagtccatagccgagtccctcagctccctgggcaccgactc
atccgactctgacgtggattacgacttccttaacgactggggacccaggtttaagatgct
ggctgagctgtacggctcggacccccgggaggagctgctgtattaggcggccgaggtcac
tctgggcctggggacccaaaccccctgcagcccaggccagtcagactccaggcaccacag
cvncadctccaaaaatggcagtgactccccagcccagcaccccttcctcgtgggtcccag
agacctcatcagccttgggatagcaaactccaggttcctgaaatatccaggaatatatgt
cagtgatgactattctcaaatgctggcaaatccaggctggtgttctgtctgggctcagac
atccacataaccctgtcacccacagaccgccgtctaactcaaagacttcctctggctccc
caaggctgcaaagcaaaacagactgtgtttaactgctgcagggtctttttctagggtccc
tgaacgccctggtaaggctggtgaggtcctggtgcctatctgcctggaggcaaaggcctg
gacagcttgacttgtggggcaggattctctgcagcccattcccaagggagactgaccatc


  [Part of this file has been deleted for brevity]

tacggttcctcgtgggctgctacatgtcgcacacgcgcaaggcggtgatgccggtggtcg
agcgcgccgacgcgctgctctgctacccgaccccctacgagggcttcgagtattcgccga
acatcgtctacggcggtccggcgccgaaccagaacagtgcgccgctggcggcgtacctga
ttcgccactacggcgagcgggtggtgttcatcggctcggactacatctatccgcgggaaa
gcaaccatgtgatgcgccacctgtatcgccagcacggcggcacggtgctcgaggaaatct
acattccgctgtatccctccgacgacgacttgcagcgcgccgtcgagcgcatctaccagg
cgcgcgccgacgtggtcttctccaccgtggtgggcaccggcaccgccgagctgtatcgcg
ccatcgcccgtcgctacggcgacggcaggcggccgccgatcgccagcctgaccaccagcg
aggcggaggtggcgaagatggagagtgacgtggcagaggggcaggtggtggtcgcgcctt
acttctccagcatcgatacgcccgccagccgggccttcgtccaggcctgccatggtttct
tcccggagaacgcgaccatcaccgcctgggccgaggcggcctactggcagaccttgttgc
tcggccgcgccgcgcaggccgcaggcaactggcgggtggaagacgtgcagcggcacctgt
acgacatcgacatcgacgcgccacaggggccggtccgggtggagcgccagaacaaccaca
gccgcctgtcttcgcgcatcgcggaaatcgatgcgcgcggcgtgttccaggtccgctggc
agtcgcccgaaccgattcgccccgacccttatgtcgtcgtgcataacctcgacgactggt
ccgccagcatgggcgggggaccgctcccatgagcgccaactcgctgctcggcagcctgcg
cgagttgcaggtgctggtcctcaacccgccgggggaggtcagcgacgccctggtcttgca
gctgatccgcatcggttgttcggtgcgccagtgctggccgccgccggaagccttcgacgt
gccggtggacgtggtcttcaccagcattttccagaatggccaccacgacgagatcgctgc
gctgctcgccgccgggactccgcgcactaccctggtggcgctggtggagtacgaaagccc
cgcggtgctctcgcagatcatcgagctggagtgccacggcgtgatcacccagccgctcga
tgcccaccgggtgctgcctgtgctggtatcggcgcggcgcatcagcgaggaaatggcgaa
gctgaagcagaagaccgagcagctccaggaccgcatcgccggccaggcccggatcaacca
ggccaaggtgttgctgatgcagcgccatggctgggacgagcgcgaggcgcaccagcacct
gtcgcgggaagcgatgaagcggcgcgagccgatcctgaagatcgctcaggagttgctggg
aaacgagccgtccgcctgagcgatccgggccgaccagaacaataacaagaggggtatcgt
catcatgctgggactggttctgctgtacgttggcgcggtgctgtttctcaatgccgtctg
gttgctgggcaagatcagcggtcgggaggtggcggtgatcaacttcctggtcggcgtgct
gagcgcctgcgtcgcgttctacctgatcttttccgcagcagccgggcagggctcgctgaa
ggccggagcgctgaccctgctattcgcttttacctatctgtgggtggccgccaaccagtt
cctcgag
>X77161 X77161.1 Pseudomonas aeruginosa (PAC1) amiS gene.
gagccgtccgcctgagcgatccgggccgaccagaacaataacaagaggggtatcgtcatc
atgctgggactggttctgctgtacgttggcgcggtgctgtttctcaatgccgtctggttg
ctgggcaagatcagcggtcgggaggtggcggtgatcaacttcctggtcggcgtgctgagc
gcctgcgtcgcgttctacctgatcttttccgcagcagccgggcagggctcgctgaaggcc
ggagcgctgaccctgctattcgcttttacctatctgtgggtggccgccaaccagttcctc
gaggtggacggcaagggcctcggctggttctgcctgttcgtcagcctcaccgcctgcacc
gtggcgatcgagtcgttcgccggcgccagtggtccgttcggcctgtggaacgcggtcaac
tggacagtctgggcgttgctctggttctgtttcttcctgctgctggggctgtcccgcggc
atccagaagccggtggcctacctgaccctggccagcgccatattcaccgcctggttgccc
ggcctgctgctgctcggacaggtgctcaaggcatagcaggaagtcggaaagggatgacgg
cttgccgccatcccgtcccttccgaacgcctagccgagcggccagttgatcaccacgacg
gcgtcgttgtagtcgttgtcggtgccgtcttcagagccgaccagggcgaagttcagctcg
ttggtcaggattacctgtgccgagaccagatccgaggggcggccgttgacgctgacctgg
acctgtaccttgccactgctgccggagttgagcacctgggtgccgatgacggcgttattg
gtgctttgcccgctgaaggtcgcggccgtgctcgttgttgaccagcacgttcaccgtctg
ggttccggacgagttggcgaaggcggtgacgccggaacctggttgttggcgggaagggtg
aacactccttgtggttgccatggtggtatctccactgaatacctggccccttccttttca
ggcagccgtctggcgcgcggtatggcgtgtcgggagaaatccgcagtccttggcggcagg
cgatgcgcaggcaggaaggacgcatcgttcagccaatctacgccgtcgac

Data files

   None

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
                    banana       Plot bending and curvature data for B-DNA
                    btwisted     Calculate the twisting in a B-DNA sequence
                    chaos        Draw a chaos game representation plot for a nucleotide sequence
                    compseq      Calculate the composition of unique words in sequences
                    dan          Calculates nucleic acid melting temperature
                    density      Draw a nucleic acid density plot
                    freak        Generate residue/base frequency table or plot
                    isochore     Plots isochores in DNA sequences
                    sirna        Finds siRNA duplexes in mRNA
                    wordcount    Count and extract unique words in molecular sequence(s)

Author(s)

Target users

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

Comments

                    None
