|   | complex | 
| % complex -omnia Find the linguistic complexity in nucleotide sequences Input nucleotide sequence(s): tembl:* Window length [100]: Step size [5]: Minimum word length [4]: Maximum word length [6]: Output file [hs989235.complex]: output sequence(s) [hs989235.fasta]: | 
Go to the input files for this example
Go to the output files for this example
| 
   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 (Any integer value)
   -step               integer    [5] Displacement of the window over the
                                  sequence (Any integer value)
   -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] Output file name
*  -outseq             seqoutall  [ | 
| Standard (Mandatory) qualifiers | Allowed values | Default | |
|---|---|---|---|
| [-sequence] (Parameter 1) | Nucleotide sequence(s) filename and optional format, or reference (input USA) | Readable sequence(s) | Required | 
| -lwin | Window length | Any integer value | 100 | 
| -step | Displacement of the window over the sequence | Any integer value | 5 | 
| -jmin | Minimum word length | Integer from 2 to 20 | 4 | 
| -jmax | Maximum word length | Integer from 2 to 50 | 6 | 
| [-outfile] (Parameter 2) | Output file name | Output file | |
| -outseq | Sequence set(s) filename and optional format (output USA) | Writeable sequence(s) | |
| Additional (Optional) qualifiers | Allowed values | Default | |
| (none) | |||
| Advanced (Unprompted) qualifiers | Allowed values | Default | |
| -omnia | Calculate over a set of sequences | Toggle value Yes/No | No | 
| -sim | Calculate the linguistic complexity by comparison with a number of simulations having a uniform distribution of bases | Any integer value | 0 | 
| -freq | Execute the simulation of a sequence based on the base frequency of the original sequence | Boolean value Yes/No | No | 
| 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 | Program complex temporary output file | Output file | complex.ujtable | 
|  | 
| 
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                    HS989235            495             0.7210 
         2                    AB009602            561             0.6688 
         3                      HSCAD5           3170             0.6921 
         4                         HSD            781             0.6991 
         5                      HSEGL1           3919             0.6618 
         6                       HSFAU            518             0.6739 
         7                      HSFAU1           2016             0.7105 
         8                       HSFOS           6210             0.6681 
         9                       HSEF2           3075             0.6925 
        10                        HSHT           1658             0.7314 
        11                       HSTS1          18596             0.6668 
        12                      HSNFG9          33760             0.6661 
        13                    AB000095           2399             0.6569 
        14                    AB009062            532             0.6465 
        15                     HSFERG1            512             0.5609 
        16                     HSFERG2           1132             0.7217 
        17                    AC004629         116019             0.6478 
        18                    AP000504         100000             0.6611 
        19                    AF129756         184666             0.6562 
        20                    AB000360           2582             0.6710 
        21                       HSHBB          73308             0.6544 
        22                     CEZK637          40699             0.6307 
        23                      PDRHOD           1675             0.6201 
        24                    AAHSP70B           4712             0.7110 
        25                      GMGL01           3400             0.3981 
        26                    GMLLBPS1            852             0.5986 
        27                    GMLLBPS2           1698             0.5225 
        28                       ECLAC           7477             0.7137 
        29                      ECLACA           1832             0.6916 
        30                      ECLACI           1113             0.7480 
        31                      ECLACY           1500             0.6801 
        32                      ECLACZ           3078             0.7278 
        33                      PAAMIB           1212             0.6596 
        34                      PAAMIE           1065             0.6418 
        35                      PAAMIR           2167             0.6562 
        36                      PAAMIS           1130             0.6989 
        37                        MMAM            366             0.7163 
        38                       RNOPS           1493             0.6571 
        39                    RNU68037           1218             0.6381 
        40                   HSA203YC1            389             0.4327 
        41                     HHTETRA           1272             0.3114 
        42                    XLRHODOP           1684             0.7193 
        43                     XL23808           4734             0.7180 
        44                    AF123456           1510             0.5913 
        45                    AF123457           1634             0.7254 
 | 
| >HS989235 H45989.1 yo13c02.s1 Soares adult brain N2b5HB55Y Homo sapiens cDNA clone IMAGE:177794 3', mRNA sequence. ccggnaagctcancttggaccaccgactctcgantgnntcgccgcgggagccggntggan aacctgagcgggactggnagaaggagcagagggaggcagcacccggcgtgacggnagtgt gtggggcactcaggccttccgcagtgtcatctgccacacggaaggcacggccacgggcag gggggtctatgatcttctgcatgcccagctggcatggccccacgtagagtggnntggcgt ctcggtgctggtcagcgacacgttgtcctggctgggcaggtccagctcccggaggacctg gggcttcagcttcccgtagcgctggctgcagtgacggatgctcttgcgctgccatttctg ggtgctgtcactgtccttgctcactccaaaccagttcggcggtccccctgcggatggtct gtgttgatggacgtttgggctttgcagcaccggccgccgagttcatggtngggtnaagag atttgggttttttcn >AB009602 AB009602.1 Schizosaccharomyces pombe mRNA for MET1 homolog, partial cds. gttcgatgcctaaaataccttcttttgtccctacacagaccacagttttcctaatggctt tacaccgactagaaattcttgtgcaagcactaattgaaagcggttggcctagagtgttac cggtttgtatagctgagcgcgtctcttgccctgatcaaaggttcattttctctactttgg aagacgttgtggaagaatacaacaagtacgagtctctcccccctggtttgctgattactg gatacagttgtaatacccttcgcaacaccgcgtaactatctatatgaattattttccctt tattatatgtagtaggttcgtctttaatcttcctttagcaagtcttttactgttttcgac ctcaatgttcatgttcttaggttgttttggataatatgcggtcagtttaatcttcgttgt ttcttcttaaaatatttattcatggtttaatttttggtttgtacttgttcaggggccagt tcattatttactctgtttgtatacagcagttcttttatttttagtatgattttaatttaa aacaattctaatggtcaaaaa >HSCAD5 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 [Part of this file has been deleted for brevity] gagccagttgtcaagaagagcagcagcagcagctcctgtctcctgcaggacagcagcagc cctgctcactccacgagcacggtggcagcagcagcagcgagcgcaccaccagagggacgg atgctcattcaggacatcccttccatccccagcagagggcacttggagagcacgtctgat ttggttgtggactccacctactacagcagtttttaccagccatccctgtatccttactat aacaacctgtacaactactcccagtaccaaatggcagtggccactgagtcttcctcaagt gagacagggggtacgtttgtagggtcagccatgaaaaacagccttcgaagcctcccagca acatacatgtcaagccagtcaggaaaacagtggcagatgaagggaatggagaaccgccat gccatgagctcccagtaccggatgtgctcctactacccgcccacctcatacctgggccag ggggttggcagtcccacctgcgtcacacagatactggcctcggaggacaccccctcctac tcagagtcgaaagcgagagtgttttcgccgcccagcagccaggactcgggcctggggtgc ctgtcgagcagcgagagcaccaagggagacctggagtgcgagccccaccaagagcccggc gccttcgcggtgagcccggttcttgagggcgagtaggcgcggcgtcgggcggctgctgcg cggcgttcactgttgccttgttctgttggggttgcgggggggcgttgggtttcttctttc cggggcggggggggcacggcggggccgcggccgggccggcggggcggggcggggcgggac ggggcggggcggagccgcgcgggggccgcagtccgggccggggccgccgtcgggtctcgg cccgctcccgtcggggcggagcgtccgacgatcggcctccacgaaacgcggtgccgtgat gtgtttgtagtggttcctcgtaggctccagacgttttctcctcgtatcgccaaattaacg cgttttgcatattacagttgagtgcctcgacttagattgcaatataagcggccagcaaac aagtctcaaaaaaaagttacgtgcgtttctgcgagtgttattttgttaagaacggctcac agtgtcctcttcctgtgttacagaagccaacctgaaatgaaactagtctggaaaaattca ttgttctctgtagttgcagctgtacctgaaataaaaatgttattgatgactgaaaaaaaa aaaaaaaaaa >AF123457 AF123457.1 Toxoplasma gondii enolase (ENO2) mRNA, complete cds. tctaccgttactcaacttccaacaaaatggtggccatcaaggacatcactgctcgtcaga tcctcgactcccgaggaaacccgaccgtcgaggttgacttgttgaccgatggcggctgct tccgtgccgctgtccccagcggcgcatccactggcatctacgaggcgcttgagctccgtg acaaggaccaaactaagttcatgggcaagggtgtgatgaaggccgtggagaacatccaca agattatcaagccggcgcttattggcaaggacccgtgcgaccagaagggtattgacaagc tgatggtcgaggagctcgatggaactaagaacgagtggggctggtgcaagtcgaagctcg gcgcgaacgcgatcctggccgtctcgatggcttgctgccgcgccggcgctgctgccaagg gcatgcccctgtacaagtacattgccactttggctggaaacccgacagacaagatggtaa tgcccgtcccgttcttcaacgtcatcaacggcggctcccacgcaggcaacaaggtcgcga tgcaggagttcatgatcgcccccgtcggcgcctccacaatccaagaggcgatccagatcg gcgcggaagtgtaccagcacctgaaggtcgtcattaagaagaagtatggcctcgacgcca cgaacgtcggcgacgagggtggcttcgcccccaacatcagcggcgccacggaggccctcg acttgctgatggaggccatcaaggtgtctggtcacgaaggcaaggtcaagattgccgccg acgtcgccgcttccgagttcttcctccaggacgacaaagtctatgacctagacttcaaga ctccgaacaacgacaagtcgcaacgcaagactggcgaagagcttcgcaacctgtacaagg acctgtgccagaagtatcccttcgtgtccatcgaggacccgttcgaccaggacgacttcc acagctacgctcagctcaccaacgaggttggcgagaaggtccaaatcgtcggcgacgacc tcctggtcaccaacccgacgcgcattgagaaggccgttcaggagaaagcgtgcaacggcc tgcttctcaaggtgaaccagattggcacagtcagcgagtctatcgaggcctgccagcttg cccagaagaacaagtggggcgttatggtttctcaccgctccggtgagactgaggactcct tcatcgctgacctcgtcgtcggtctccgcaccgggcaaatcaagactggcgccccgtgca gatccgagcgtctctgcaagtacaaccagctgatgcgtatcgaagagtcgctcggctccg actgtcagtacgccggcgctggcttccgccatcccaactaagtggaaacggagtttcgac tacccaactgctcaattggggctgggtggtttgtccactctgcaacaagggcgtgacgag atcgttgcacatgcaactgccttttttgtgcttggtgggaaggagcactttcgcaggtgc agcaccgagttgcggttgatgggaatttcggaactgatttgtttcttgcatgccatcacc gaaggaacgagcagtttcgttgataatattggaaagtcttttgaaaaaaaaaaaaaaaaa aaaaaaaaaaaaaa | 
| Program name | Description | 
|---|---|
| banana | Bending and curvature plot in B-DNA | 
| btwisted | Calculates the twisting in a B-DNA sequence | 
| chaos | Create a chaos game representation plot for a sequence | 
| compseq | Count composition of dimer/trimer/etc words in a sequence | 
| dan | Calculates DNA RNA/DNA melting temperature | 
| freak | Residue/base frequency table or plot | 
| isochore | Plots isochores in large DNA sequences | 
| sirna | Finds siRNA duplexes in mRNA | 
| wordcount | Counts words of a specified size in a DNA sequence |