Bio::Tools::Run::PiseApplication::consensus Bio::Tools::Run::PiseApplication::consensus is a Perl module.
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Perl module UNALIGNED unaligned DNA protein sequences DNA

Bio::Tools::Run::PiseApplication::consensus Description

Bio::Tools::Run::PiseApplication::consensus is a Perl module. Bio::Tools::Run::PiseApplication::consensus is a Perl module.Bioperl class for: CONSENSUS Identification of consensus patterns in unaligned DNA and protein sequences (Hertz, Stormo) References: 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. Parameters: (see also: http://bioweb.pasteur.fr/seqanal/interfaces/consensus.html for available values): consensus (Excl) Program to run sequence (Sequence) Sequences file (-f) pipe: seqsfile width (Integer) Width of pattern (consensus only) (-L) out (String) consensus_matrix (String) complement (Excl) Complement of nucleic acid sequences (-c) ascii_alphabet (InFile) Alphabet and normalization information (if not DNA) (-a) prior (Switch) Use the designated prior probabilities of the letters to override the observed frequencies (-d) dna (Switch) Alphabet and normalization information for DNA protein (Switch) Alphabet and normalization information for protein queue (Integer) Maximum number of matrices to save between cycles of the program -- ie: queue size (-q) standard_deviation (Float) Number of standard deviations to lower the information content at each position before identifying information peaks (mandatory for wconsensus) (-s) progeny (Excl) Save the top progeny matrices (-pr1) linearly (Switch) Seed with the first sequence and proceed linearly through the list (-l) max_cycle_nb (Integer) Maximum repeat of the matrix building cycle (-n or -N) max_cycle (Excl) How many words per matrix for each sequence to contribute (-n or -N) distance (Integer) Minimum distance between the starting points of words within the same matrix pattern (-m) terminate (Integer) Terminate the program this number of cycles after the current most significant alignment is identified (-t) terminal_gap (Excl) Permit terminal gaps (-pg) (wconsensus only) top_matrices (Integer) Number of top matrices to print (-pt) final_matrices (Integer) Number of final matrices to print (-pf) Requirements: · Perl

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