complex 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:* 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 Command line arguments 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 [.] 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 standard output -filter boolean Read standard input, write 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. 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 Input file format Input files for usage example 'tembl:*' 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: hs989235.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 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 File: hs989235.fasta >HS989235 H45989.1 yo13c02.s1 Soares adult brain N2b5HB55Y Homo sapiens cDNA cl one IMAGE:177794 3', mRNA sequence. ccggnaagctcancttggaccaccgactctcgantgnntcgccgcgggagccggntggan aacctgagcgggactggnagaaggagcagagggaggcagcacccggcgtgacggnagtgt gtggggcactcaggccttccgcagtgtcatctgccacacggaaggcacggccacgggcag gggggtctatgatcttctgcatgcccagctggcatggccccacgtagagtggnntggcgt ctcggtgctggtcagcgacacgttgtcctggctgggcaggtccagctcccggaggacctg gggcttcagcttcccgtagcgctggctgcagtgacggatgctcttgcgctgccatttctg ggtgctgtcactgtccttgctcactccaaaccagttcggcggtccccctgcggatggtct gtgttgatggacgtttgggctttgcagcaccggccgccgagttcatggtngggtnaagag atttgggttttttcn >AB009602 AB009602.1 Schizosaccharomyces pombe mRNA for MET1 homolog, partial c ds. 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 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 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 Author(s) Target users This program is intended to be used by everyone and everything, from naive users to embedded scripts. Comments None