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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