Bio::Tools::Run::PiseApplication::consensus 1.4

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)