|   | complex | 
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| % 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
| 
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  [ | 
| 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 | 
| -lwin | integer | Window length | Integer 1 or more | 100 | 
| -step | integer | Displacement of the window over the sequence | Integer 1 or more | 5 | 
| -jmin | integer | Minimum word length | Integer from 2 to 20 | 4 | 
| -jmax | integer | Maximum word length | Integer from 2 to 50 | 6 | 
| [-outfile] (Parameter 2) | outfile | Program complex output file | Output file | <*>.complex | 
| -outseq | seqoutall | Sequence set(s) filename and optional format (output USA) | Writeable sequence(s) | <*>.format | 
| Additional (Optional) qualifiers | ||||
| (none) | ||||
| Advanced (Unprompted) qualifiers | ||||
| -omnia | toggle | Calculate over a set of sequences | Toggle value Yes/No | No | 
| -sim | integer | Calculate the linguistic complexity by comparison with a number of simulations having a uniform distribution of bases | Any integer value | 0 | 
| -freq | boolean | Execute the simulation of a sequence based on the base frequency of the original sequence | Boolean value Yes/No | No | 
| boolean | Generate a file named UjTable containing the values of Uj for each word j in the real sequence(s) and in any simulated sequences | Boolean value Yes/No | No | |
| -ujtablefile | outfile | Program complex temporary output file | Output file | complex.ujtable | 
| 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 | 
| -sask1 -sask_sequence | 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 outfile qualifiers | ||||
| -odirectory2 -odirectory_outfile | string | Output directory | Any string | |
| "-ujtablefile" associated outfile qualifiers | ||||
| -odirectory | string | Output directory | Any string | |
| "-outseq" associated seqoutall qualifiers | ||||
| -osformat | string | Output seq format | Any string | |
| -osextension | string | File name extension | Any string | |
| -osname | string | Base file name | Any string | |
| -osdirectory | string | Output directory | Any string | |
| -osdbname | string | Database name to add | Any string | |
| -ossingle | boolean | Separate file for each entry | Boolean value Yes/No | N | 
| -oufo | string | UFO features | Any string | |
| -offormat | string | Features format | Any string | |
| -ofname | string | Features file name | Any string | |
| -ofdirectory | 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 | 
| -error | boolean | Report errors | 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 | 
|  | 
| 
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 
 | 
| >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 | 
| 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) |