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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 |
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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 |