]> Counts the composition of dimer/trimer/etc words in a sequence (EMBOSS) nucleic:composition protein:composition http://bioweb.pasteur.fr/docs/EMBOSS/compseq.html compseq &emboss_init; input Input section sequence sequence -- any [sequences] (-sequence) perl " -sequence=$value -sformat=fasta" 1 any 8 seqsfile perl 1 required Required section word Word size to consider (e.g. 2=dimer) (-word) 2 perl " -word=$value" 2 This is the size of word (n-mer) to count. <BR> Thus if you want to count codon frequencies, you should enter 3 here. 1 20 advanced Advanced section infile 'compseq' file to use for expected word frequencies (-infile) perl ($value)? " -infile=$value" : "" 3 This is a file previously produced by 'compseq' that can be used to set the expected frequencies of words in this analysis. <BR> The word size in the current run must be the same as the one in this results file. Obviously, you should use a file produced from protein sequences if you are counting protein sequence word frequencies, and you must use one made from nucleotide frequencies if you and analysing a nucleotide sequence. frame Frame of word to look at (0=all frames) (-frame) 0 perl (defined $value && $value != $vdef)? " -frame=$value" : "" 4 The normal behaviour of 'compseq' is to count the frequencies of all words that occur by moving a window of length 'word' up by one each time. <BR> This option allows you to move the window up by the length of the word each time, skipping over the intervening words. <BR> You can count only those words that occur in a single frame of the word by setting this value to a number other than zero. <BR> If you set it to 1 it will only count the words in frame 1, 2 will only count the words in frame 2 and so on. acd $word ignorebz Ignore the amino acids B and Z and just count them as 'Other' (-ignorebz) 1 perl ($value)? "" : " -noignorebz" 5 The amino acid code B represents Asparagine or Aspartic acid and the code Z represents Glutamine or Glutamic acid. <BR> These are not commonly used codes and you may wish not to count words containing them, just noting them in the count of 'Other' words. reverse Count words in the forward and reverse sense (-reverse) 0 perl ($value)? " -reverse" : "" 6 Set this to be true if you also wish to also count words in the reverse complement of a nucleic sequence. output Output section outfile outfile (-outfile) outfile.out perl " -outfile=$value" 7 This is the results file. zerocount Display the words that have a frequency of zero (-zerocount) 1 perl ($value)? "" : " -nozerocount" 8 You can make the output results file much smaller if you do not display the words with a zero count. auto perl " -auto -stdout" 9