Bio::Tools::Run::PiseApplication::mview_blast(3)

NAME
Bio::Tools::Run::PiseApplication::mview_blast

SYNOPSIS
  #

DESCRIPTION
Bio::Tools::Run::PiseApplication::mview_blast

      Bioperl class for:

        MVIEW   view Blast results as a multiple alignment (N. P. Brown)

        References:

                Brown, N.P., Leroy C., Sander C. (1998). MView: A Web compatible database search or multiple alignment  viewer. Bioinformatics. 14(4):380-381.

      Parameters:

        (see also:
          http://bioweb.pasteur.fr/seqanal/interfaces/mview_blast.html
         for available values):

                mview_blast (String)

                blast_output (InFile)
                        Blast/FASTA Output File
                        pipe: blast_output
                        pipe: mview_input

                in (Excl)
                        Type of search (-in)

                ruler (Switch)
                        Attach a ruler (-ruler)

                alignment (Switch)
                        Show alignment (-alignment)

                consensus (Switch)
                        Show consensus (-consensus)

                dna (Switch)
                        Use DNA/RNA colormaps and/or consensus groups (-dna)

                coloring (Excl)
                        Colour scheme (-coloring)

                threshold (Float)
                        Threshold percentage for consensus coloring (-threshold)

                ignore (Excl)
                        Ignore singleton or class group (-ignore)

                con_coloring (Excl)
                        Basic style of coloring (-con_coloring)

                con_threshold (String)
                        Consensus line thresholds (in range 50..100) (separated by commas) (-con_threshold)

                con_ignore (Excl)
                        Ignore singleton or class group (-con_ignore)

                con_gaps (Switch)
                        Count gaps during consensus computations (-con_gaps)

                top (Integer)
                        Report top N hits (-top)

                range (String)
                        Display column range M..N as numbered by ruler (M,N) (-range)

                maxident (Integer)
                        Only report sequences with %identity <= N (-maxident)

                ref (Integer)
                        Use row N or row identifier as %id entity reference (-ref)

                keep_only (String)
                        Keep only the rows from start to end (separated by commas: start,end) (-keep)

                disc (String)
                        Discard rows from start to end (separated by commas: start,end) (-disc)

                nops (String)
                        Display rows unprocessed (separated by commas) (-nops)

                width (Integer)
                        Paginate in N columns of alignment (-width)

                gap (String)
                        Use this character as the gap (-gap)

                label0 (Switch)
                        Switch off label: row number (-label0)

                label1 (Switch)
                        Switch off label: identifier (-label1)

                label2 (Switch)
                        Switch off label: description (-label2)

                label3 (Switch)
                        Switch off label: scores (-label3)

                label4 (Switch)
                        Switch off label: percent identity (-label4)

                register (Switch)
                        Output multi-pass alignments with columns in register (-register)

                html_output (Excl)
                        HTML output

                pagecolor (String)
                        Page backgound color (-pagecolor)

                textcolor (String)
                        Page text color (-textcolor)

                linkcolor (String)
                        Link color (-linkcolor)

                alinkcolor (String)
                        Active link color (-alinkcolor)

                vlinkcolor (String)
                        Visited link color (-vlinkcolor)

                alncolor (String)
                        Alignment background color (-alncolor)

                symcolor (String)
                        Alignment default text color (-symcolor)

                gapcolor (String)
                        Alignment gap color (-gapcolor)

                bold (Switch)
                        Use bold emphasis for coloured residues (-bold)

                css (Excl)
                        Use Cascading Style Sheets (-css)

                srs (Switch)
                        Try to use SRS links (-srs)

                hsp (Excl)
                        HSP tiling method (-hsp)

                strand (Excl)
                        Report only these query strand orientations (-strand)

                maxpval (Float)
                        Ignore hits with p-value more than N -- Blastp only (-maxpval)

                minscore (Float)
                        Ignore hits with score less than N (-minscore)

                maxeval (Float)
                        Ignore hits with p-value more than N -- Blast2 only (-maxeval)

                minbits (Float)
                        Ignore hits with bits less than N (-minbits)

                cycle (String)
                        Process the Nth cycle of a multipass search (-cycle)

                minopt (Integer)
                        Ignore hits with opt score less than N (-minopt)

                fasta_strand (Excl)
                        Report only these query strand orientations (-strand)

                html_output_file (OutFile)

                out (Excl)
                        Output format (-out)

FEEDBACK
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated.

  bioperl-l@bioperl.org              - General discussion
  http://bioperl.org/MailList.shtml  - About the mailing lists
Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web:

  http://bugzilla.bioperl.org/

AUTHOR
Catherine Letondal (letondal@pasteur.fr)

COPYRIGHT
Copyright (C) 2003 Institut Pasteur & Catherine Letondal. All Rights Reserved.

This module is free software; you can redistribute it and/or modify it under the same terms as Perl itself.

DISCLAIMER
This software is provided "as is" without warranty of any kind.

SEE ALSO

•   http://bioweb.pasteur.fr/seqanal/interfaces/mview_blast.html

•   Bio::Tools::Run::PiseApplication

•   Bio::Tools::Run::AnalysisFactory::Pise

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