score the words of a sequence against an alignment matrix Hertz, Storm patser patser perl "fasta-consensus < $sequence > $sequence.wcons; patser " 0 matrix Matrix file (-m) perl " -m $value" 1 consensus_matrix perl 1 sequence Sequences file perl " -f $sequence.wcons" 1 8 control_options Control options 1 matrix_options Matrix options 1 weight Matrix is a weight matrix (-w) perl ($value)? " -w" : "" 0 1 vertical Matrix is a vertical matrix (-v) perl ($value)? " -v" : "" 0 1 correction Correction added to the elements of the alignment matrix (-b) perl (defined $value && $value != $vdef)? " -b$value" : "" 1 1 print_matrix Print the weight matrix derived from the alignment matrix (-p) perl ($value)? " -p" : "" 0 1 alphabet_options Alphabet options 1 dna Alphabet and normalization information for DNA perl ($value)? " -A a:t c:g" : "" 1 protein Alphabet and normalization information for protein perl ($value) ? " -a /local/gensoft/lib/consensus/prot-alphabet" : "" 1 1 ascii_alphabet Alphabet and normalization information (-a) perl ($value) ? " -a $value" : "" 1 Each line contains a letter (a symbol in the alphabet) followed by an optional normalization number (default: 1.0). The normalization is based on the relative prior probabilities of the letters. For nucleic acids, this might be be the genomic frequency of the bases; however, if the -d option is not used, the frequencies observed in your own sequence data are used. In nucleic acid alphabets, a letter and its complement appear on the same line, separated by a colon (a letter can be its own complement, e.g. when using a dimer alphabet). Complementary letters may use the same normalization number. Only the standard 26 letters are permissible; however, when the -CS option is used, the alphabet is case sensitive so that a total of 52 different characters are possible. POSSIBLE LINE FORMATS WITHOUT COMPLEMENTARY LETTERS: letter letter normalization POSSIBLE LINE FORMATS WITH COMPLEMENTARY LETTERS: letter:complement letter:complement normalization letter:complement normalization:complement's_normalization score Score options (-d) perl ($value && $value ne $vdef)? " -d$value" : "" 1 1 0 -d0: Treat unrecognized characters as errors 1 -d1: Treat unrecognized characters as discontinuities, but print warning 2 -d2: Treat unrecognized characters as discontinuities, and print NO warning range Range for approximating a weight matrix with integers (-R) perl (defined $value && $value != $vdef)? " -R$value" : "" 10000 1 This number is the difference between the largest and smallest integers used to estimate the scores. Higher values increase precision, but will take longer to calculate the table of p-values. min_score Minimum score for calculating the p-value of scores (-M) perl (defined $value && $value != $vdef)? " -M$value" : "" 0 1 Higher values will increase precision, but may miss interesting scores