]> COMPLEX Find the linguistic complexity in nucleotide sequences (EMBOSS) nucleic:composition http://bioweb.pasteur.fr/docs/EMBOSS/complex.html complex &emboss_init; sequence sequence -- dna [sequences] (-sequence) perl " -sequence=$value -sformat=fasta" 1 dna 8 seqsfile perl 1 omnia All sequences (-omnia) 0 perl ($value)? " -omnia" : "" 2 calculate over a set of sequences lwin Window length (-lwin) 100 perl (defined $value && $value != $vdef)? " -lwin=$value" : "" 3 acd $sequence.length step Step size (-step) 5 perl (defined $value && $value != $vdef)? " -step=$value" : "" 4 the displacement of the window over the sequence acd $lwin sim Simulations (-sim) 0 perl (defined $value && $value != $vdef)? " -sim=$value" : "" 5 calculate the linguistic complexity by comparison with a number of simulations having a uniform distribution of bases jmin Minimum word length (-jmin) 4 perl (defined $value && $value != $vdef)? " -jmin=$value" : "" 6 2 20 jmax Maximum word length (-jmax) 6 perl (defined $value && $value != $vdef)? " -jmax=$value" : "" 7 2 50 freq Calculate frequency (-freq) 0 perl ($value)? " -freq" : "" 8 execute the simulation of a sequence based on the base frequency of the original sequence print Print to file (-print) 0 perl ($value)? " -print" : "" 9 generate a file named UjTable containing the values of Uj for each word j in the real sequence(s) and in any simulated sequences outfile outfile (-outfile) outfile.out perl " -outfile=$value" 10 ujtablefile UjTable temporary file name (-ujtablefile) perl $sim acd $sim complex.ujtable perl ($value && $value ne $vdef)? " -ujtablefile=$value" : "" 11 outseq outseq (-outseq) perl $omnia acd $omnia perl ($value)? " -outseq=$value" : "" 12 seqsfile perl 1 outseq_sformat Output format for: outseq fasta gcg phylip embl swiss ncbi nbrf genbank ig codata strider acedb staden text fitch msf clustal phylip phylip3 asn1 fasta perl " -osformat=$value" 13 auto perl " -auto -stdout" 14