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complex
Wiki
The master copies of EMBOSS documentation are available at
http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki.
Please help by correcting and extending the Wiki pages.
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
|
