Bio::Tools::Run::PiseApplication::most # Bio::Tools::Run::PiseApplication::most Bioperl class for: MoST Motif Search Tool (Tatusov, Altschul, Koonin) Parameters: most (Excl) MoST program cap (Paragraph) CAP Parameters blast_output (InFile) Blast Output File capoutfile (OutFile) CAP result file criterium (Excl) Criterium noless (Integer) min height of motif (%) blast_score (Integer) min Blast score mostopt (Paragraph) MoST Parameters aadb (Excl) Protein Database block (InFile) Block file (generated by CAP) iter (Integer) how many iterations method (Excl) Method of computation of position-dependent weight matrix from alignment block seg (Switch) apply seg filter segv (Integer) width parameter (if segfilter) identical (Integer) use only one representative of each group of sequence segments that are #% or more identical tmpfile (Results)

new
Title : new() Usage : my $most = Bio::Tools::Run::PiseApplication::most->new($remote, $email, @params); Function: Creates a Bio::Tools::Run::PiseApplication::most object. This method should not be used directly, but rather by a Bio::Factory::Pise instance: my $factory = Bio::Factory::Pise->new(-email => 'me@myhome'); my $most = $factory->program('most'); Example : Returns : An instance of Bio::Tools::Run::PiseApplication::most.