Identification of consensus patterns in unaligned DNA and protein sequences Hertz, Stormo G.Z. Hertz and G.D. Stormo. Identification of consensus patterns in unaligned DNA and protein sequences: a large-deviation statistical basis for penalizing gaps. In: Proceedings of the Third International Conference on Bioinformatics and Genome Research (H.A. Lim, and C.R. Cantor, editors). World Scientific Publishing Co., Ltd. Singapore, 1995. pages 201--216. alignment:consensus consensus consensus Program to run perl "fasta-consensus < $sequence > $sequence.wcons; $consensus " consensus 0 consensus consensus: search for fixed width patterns wconsensus wconsensus: same as consensus, width not fixed sequence Sequences file (-f) perl " -f $sequence.wcons" 1 8 seqsfile perl 1 width Width of pattern (consensus only) (-L) perl (defined $value) ? " -L$value" : "" 2 perl $consensus eq "consensus" out perl " > $consensus.results" 50 consensus_matrix perl " ;consensus-matrix $consensus.results" 100 matrices $consensus.results.matrix.* consensus_matrix perl 1 results_file $consensus.results consensus_results perl 1 sequence_wcons *.wcons input_options Input options 2 complement Complement of nucleic acid sequences (-c) perl ($value)? " -c$value" : "" 0 2 0 0: ignore the complement 1 1: include both strands as separate sequences 2 2: include both strands as a single sequence 3 3: Assume that the pattern is symmetrical (consensus) 3: this choice is for the consensus program only perl $value eq "3" && $consensus eq "wconsensus" alphabet_options Alphabet options 2 ascii_alphabet perl ! $dna Alphabet and normalization information (if not DNA) (-a) perl ($value)? " -a $value" : "" 2 Each line contains a letter (a symbol in the alphabet) followed by an optional normalization number (default: 1.0). The normalization is based on the relative prior probabilities of the letters. For nucleic acids, this might be be the genomic frequency of the bases; however, if the -d option is not used, the frequencies observed in your own sequence data are used. In nucleic acid alphabets, a letter and its complement appear on the same line, separated by a colon (a letter can be its own complement, e.g. when using a dimer alphabet). Complementary letters may use the same normalization number. Only the standard 26 letters are permissible; however, when the -CS option is used, the alphabet is case sensitive so that a total of 52 different characters are possible. POSSIBLE LINE FORMATS WITHOUT COMPLEMENTARY LETTERS: letter letter normalization POSSIBLE LINE FORMATS WITH COMPLEMENTARY LETTERS: letter:complement letter:complement normalization letter:complement normalization:complement's_normalization prior Use the designated prior probabilities of the letters to override the observed frequencies (-d) perl ($value)? " -d" : "" 0 2 By default, the program uses the frequencies observed in your own sequence data for the prior probabilities of the letters. However, if the -d option is set, the prior probabilities designated by the alphabet options. If the -d option is not set, they are still used to determine the sequence alphabet, but any prior probability information is ignored. dna Alphabet and normalization information for DNA perl ($value)? " -A a:t c:g" : "" protein perl ! $dna Alphabet and normalization information for protein perl ($value)? " -a /local/gensoft/lib/consensus/prot-alphabet" : "" 1 algorithm_options Algorithm options 2 queue Maximum number of matrices to save between cycles of the program -- ie: queue size (-q) perl (defined $value && $value != $vdef)? " -q$value" : "" 200 2 standard_deviation Number of standard deviations to lower the information content at each position before identifying information peaks (mandatory for wconsensus) (-s) perl " -s$value" 1 2 perl $consensus eq "wconsensus" progeny Save the top progeny matrices (-pr1) perl ($value && $value ne $vdef)? " $value" : "" -pr2 2 -pr1 -pr1: regardless of parentage -pr2 -pr2: for each parental matrix -pr2 option prevents a strong pattern found in only a subset of the sequences from overwhelming the algorithm and eliminating other potential patterns. This undesirable situation can occur when a subset of the sequences share an evolutionary relationship not common to the majority of the sequences. linearly Seed with the first sequence and proceed linearly through the list (-l) perl ($value)? " -l" : "" 0 2 This option results in a significant speed up in the program, but the algorithm becomes dependent on the order of the sequence-file names. max_cycle_nb Maximum repeat of the matrix building cycle (-n or -N) perl "" 2 max_cycle How many words per matrix for each sequence to contribute (-n or -N) perl ($value)? " $max_cycle$max_cycle_nb" : "" 2 -n -n: allow each sequence to contribute zero or more words per matrix -N -N: allow each sequence to contribute one or more words per matrix perl defined $max_cycle_nb distance Minimum distance between the starting points of words within the same matrix pattern (-m) perl (defined $value) ? " -m$value " : "" 2 For wconsensus, the default value is 1. For consensus, this number is indicated by the width (-L). This number must be positive perl $value <= 0 perl $max_cycle ne "" terminate Terminate the program this number of cycles after the current most significant alignment is identified (-t) perl (defined $value)? " -t$value " : "" 2 default: terminate only when the maximum number of matrix building cycles is completed. terminal_gap Permit terminal gaps (-pg) (wconsensus only) perl ($value && $value ne $vdef) ? " $value" : "" -pg0 2 -pg0 -pg0: do NOT permit terminal gaps -pg1 -pg1: permit penalized terminal gaps perl $consensus eq "wconsensus" output_options Output options 2 top_matrices Number of top matrices to print (-pt) perl ($value && $value != $vdef) ? " -pt$value" : "" 4 2 A negative value means print all the top matrices. final_matrices Number of final matrices to print (-pf) perl ($value && $value != $vdef) ? " -pf$value" : "" 4 2 Default when NOT using -n or -N option: print 4 matrices; default when using -n or -N option: print no matrices.