bio 0.7.0

data/lib/bio/util/sirna.rb

@@ -0,0 +1,306 @@
+#
+# = bio/util/sirna.rb - Class for designing small inhibitory RNAs
+#
+# Copyright::   Copyright (C) 2004, 2005
+#               Itoshi NIKAIDO <dritoshi@gmail.com>
+# License::     LGPL
+#
+# $Id: sirna.rb,v 1.6 2005/11/14 15:44:30 nakao Exp $
+#
+# == Bio::SiRNA - Designing siRNA.
+#
+# This class implements the selection rules described by Kumiko Ui-Tei
+# et al. (2004) and Reynolds et al. (2004).
+#
+# == Example
+#
+#  seq = Bio::Sequence::NA.new(ARGF.read)
+#  
+#  sirna = Bio::SiRNA.new(seq)
+#  pairs = sirna.design
+#  
+#  pairs.each do |pair|
+#    puts pair.report
+#    shrna = Bio::SiRNA::ShRNA.new(pair)
+#    shrna.design
+#    puts shrna.report
+#    
+#    puts shrna.top_strand.dna
+#    puts shrna.bottom_strand.dna
+#  end
+#
+# == References
+# 
+# * Kumiko Ui-Tei et al.  Guidelines for the selection of highly effective
+#   siRNA sequences for mammalian and chick RNA interference.
+#   Nucl. Acids. Res. 2004 32: 936-948.
+#    
+# * Angela Reynolds et al.  Rational siRNA design for RNA interference.
+#   Nature Biotech. 2004 22: 326-330.
+#
+#--
+#
+#  This library is free software; you can redistribute it and/or
+#  modify it under the terms of the GNU Lesser General Public
+#  License as published by the Free Software Foundation; either
+#  version 2 of the License, or (at your option) any later version.
+#
+#  This library is distributed in the hope that it will be useful,
+#  but WITHOUT ANY WARRANTY; without even the implied warranty of
+#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+#  Lesser General Public License for more details.
+#
+#  You should have received a copy of the GNU Lesser General Public
+#  License along with this library; if not, write to the Free Software
+#  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA
+#
+#++
+#
+
+require 'bio/sequence'
+
+module Bio
+
+  # = Bio::SiRNA
+  # Designing siRNA.
+  #
+  # This class implements the selection rules described by Kumiko Ui-Tei
+  # et al. (2004) and Reynolds et al. (2004).
+  class SiRNA
+
+    # A parameter of size of antisense.
+    attr_accessor :antisense_size
+
+    # A parameter of maximal %GC.
+    attr_accessor :max_gc_percent
+
+    # A parameter of minimum %GC.
+    attr_accessor :min_gc_percent
+
+    # Input is a Bio::Sequence::NA object (the target sequence).
+    # Output is a list of Bio::SiRNA::Pair object.
+    def initialize(seq, antisense_size = 21, max_gc_percent = 60.0, min_gc_percent = 40.0)
+      @seq = seq.rna!
+      @pairs = Array.new
+      @antisense_size = antisense_size
+      @max_gc_percent = max_gc_percent
+      @min_gc_percent = min_gc_percent
+    end
+
+    # Ui-Tei's rule.
+    def uitei?(target)
+      return false unless /^.{2}[GC]/i =~ target
+      return false unless /[AU].{2}$/i =~ target
+      return false if     /[GC]{9}/i   =~ target
+
+      one_third  = target.size * 1 / 3
+      start_pos  = @target_size - one_third - 1
+      remain_seq = target.subseq(start_pos, @target_size - 2)
+      gc_number  = remain_seq.scan(/[AU]/i).size
+      return false if gc_number < 5
+  
+      return true
+    end
+
+    # Reynolds' rule.
+    def reynolds?(target)
+      return false if /[GC]{9}/i =~ target
+      return false unless /^.{4}A.{6}U.{2}[AUC].{5}[AU].{2}$/i =~ target
+      return true
+    end
+
+    # same as design('uitei').
+    def uitei
+      design('uitei')
+    end
+
+    # same as design('reynolds').
+    def reynolds
+      design('reynolds')
+    end
+
+    #  rule can be one of 'uitei' (default) and 'reynolds'.
+    def design(rule = 'uitei')
+      @target_size = @antisense_size + 2
+
+      target_start = 0
+      @seq.window_search(@target_size) do |target|
+        antisense = target.subseq(1, @target_size - 2).complement.rna
+        sense     = target.subseq(3, @target_size)
+
+        target_start += 1
+        target_stop  = target_start + @target_size
+
+        antisense_gc_percent = antisense.gc_percent
+        next if antisense_gc_percent > @max_gc_percent
+        next if antisense_gc_percent < @min_gc_percent
+        
+        case rule
+        when 'uitei'
+          next unless uitei?(target)
+        when 'reynolds'
+          next unless reynolds?(target)
+        else
+          raise NotImplementedError
+        end
+
+        pair = Bio::SiRNA::Pair.new(target, sense, antisense, target_start, target_stop, rule, antisense_gc_percent)
+        @pairs.push(pair)
+      end
+      return @pairs
+    end
+
+    # = Bio::SiRNA::Pair
+    class Pair
+
+      attr_accessor :target
+
+      attr_accessor :sense
+
+      attr_accessor :antisense
+
+      attr_accessor :start
+
+      attr_accessor :stop
+
+      attr_accessor :rule
+
+      attr_accessor :gc_percent
+
+      def initialize(target, sense, antisense, start, stop, rule, gc_percent)
+        @target     = target
+        @sense      = sense
+        @antisense  = antisense
+        @start      = start
+        @stop       = stop
+        @rule       = rule
+        @gc_percent = gc_percent
+      end
+
+      # human readable report
+      def report
+        report =  "### siRNA\n"
+        report << 'Start: ' + @start.to_s + "\n"
+        report << 'Stop:  ' + @stop.to_s  + "\n"
+        report << 'Rule:  ' + @rule.to_s  + "\n"
+        report << 'GC %:  ' + @gc_percent.to_s  + "\n"
+        report << 'Target:    '        + @target.upcase + "\n"
+        report << 'Sense:     ' + '  ' + @sense.upcase  + "\n"
+        report << 'Antisense: '        + @antisense.reverse.upcase + "\n"
+      end
+
+      # computer parsable report
+      #def to_s
+      #  [ @antisense, @start, @stop ].join("\t")
+      #end
+
+    end # class Pair
+
+
+    # = Bio::SiRNA::ShRNA
+    # Designing shRNA.
+    class ShRNA
+
+      # aBio::Sequence::NA
+      attr_accessor :top_strand
+
+      # aBio::Sequence::NA
+      attr_accessor :bottom_strand
+
+      # Input is a Bio::SiRNA::Pair object (the target sequence).    
+      def initialize(pair)
+        @pair = pair
+      end
+
+      # only the 'BLOCK-iT' rule is implemented for now.
+      def design(method = 'BLOCK-iT')
+        case method
+        when 'BLOCK-iT'
+          block_it
+        else
+          raise NotImplementedError
+        end
+      end
+
+
+      # same as design('BLOCK-iT').
+      # method can be one of 'piGENE' (default) and 'BLOCK-iT'.
+      def block_it(method = 'piGENE')
+        top = Bio::Sequence::NA.new('CACC') # top_strand_shrna_overhang
+        bot = Bio::Sequence::NA.new('AAAA') # bottom_strand_shrna_overhang
+        fwd = @pair.sense
+        rev = @pair.sense.complement
+
+        case method
+        when 'BLOCK-iT'
+          # From BLOCK-iT's manual
+          loop_fwd = Bio::Sequence::NA.new('CGAA')
+          loop_rev = loop_fwd.complement
+        when 'piGENE'
+          # From piGENE document
+          loop_fwd = Bio::Sequence::NA.new('GTGTGCTGTCC')
+          loop_rev = loop_fwd.complement
+        else
+          raise NotImplementedError
+        end
+
+        if /^G/i =~ fwd
+          @top_strand    = top + fwd + loop_fwd + rev
+          @bottom_strand = bot + fwd + loop_rev + rev
+        else
+          @top_strand    = top + 'G' + fwd + loop_fwd + rev
+          @bottom_strand = bot + fwd + loop_rev + rev + 'C'
+        end
+      end
+      
+      # human readable report
+      def report
+        report = "### shRNA\n"
+        report << "Top strand shRNA (#{@top_strand.length} nt):\n"
+        report << "  5'-#{@top_strand.upcase}-3'\n"
+        report << "Bottom strand shRNA (#{@bottom_strand.length} nt):\n"
+        report << "      3'-#{@bottom_strand.reverse.upcase}-5'\n"
+      end
+
+    end # class ShRNA
+
+  end # class SiRNA
+
+end # module Bio
+
+
+if __FILE__ == $0
+  
+  seq = Bio::Sequence::NA.new(ARGF.read)
+
+  sirna = Bio::SiRNA.new(seq)
+  pairs = sirna.design # or .design('uitei') or .uitei or .reynolds
+
+  pairs.each do |pair|
+    puts pair.report
+
+    shrna = Bio::SiRNA::ShRNA.new(pair)
+    shrna.design # or .design('BLOCK-iT') or .block_it
+    puts shrna.report
+
+    puts "# as DNA"
+    puts shrna.top_strand.dna
+    puts shrna.bottom_strand.dna
+  end
+
+end  
+
+=begin
+
+= ChangeLog
+
+  2005/03/21 Itoshi NIKAIDO <itoshi.nikaido@nifty.com>
+  Bio::SiRNA#ShRNA_designer method was changed design method.
+
+  2004/06/25
+  Bio::ShRNA class was added.
+
+  2004/06/17 Itoshi NIKAIDO <itoshi.nikaido@nifty.com>
+  We can use shRNA loop sequence from piGene document.
+
+=end

data/lib/bioruby.rb

@@ -0,0 +1,34 @@
+#
+# = bioruby.rb - Loading all BioRuby modules and setup for shell programming
+#
+# Copyright::	Copyright (C) 2005
+#		Toshiaki Katayama <k@bioruby.org>
+# License::	LGPL
+#
+# $Id: bioruby.rb,v 1.1 2005/12/07 05:12:06 k Exp $
+#
+#--
+#
+#  This library is free software; you can redistribute it and/or
+#  modify it under the terms of the GNU Lesser General Public
+#  License as published by the Free Software Foundation; either
+#  version 2 of the License, or (at your option) any later version.
+#
+#  This library is distributed in the hope that it will be useful,
+#  but WITHOUT ANY WARRANTY; without even the implied warranty of
+#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+#  Lesser General Public License for more details.
+#
+#  You should have received a copy of the GNU Lesser General Public
+#  License along with this library; if not, write to the Free Software
+#  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA
+#
+#++
+#
+
+require 'bio/shell'
+
+include Bio::Shell
+
+Bio::Shell.setup
+

data/sample/biofetch.rb

@@ -0,0 +1,475 @@
+#!/usr/proj/bioruby/bin/ruby
+#
+# biofetch.rb : BioFetch server (interface to GenomeNet/DBGET via KEGG API)
+#
+#   Copyright (C) 2002-2004 KATAYAMA Toshiaki <k@bioruby.org>
+#
+#  This program is free software; you can redistribute it and/or modify
+#  it under the terms of the GNU General Public License as published by
+#  the Free Software Foundation; either version 2 of the License, or
+#  (at your option) any later version.
+#
+#  This program is distributed in the hope that it will be useful,
+#  but WITHOUT ANY WARRANTY; without even the implied warranty of
+#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#  GNU General Public License for more details.
+#
+#  You should have received a copy of the GNU General Public License
+#  along with this program; if not, write to the Free Software
+#  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
+#
+#  $Id: biofetch.rb,v 1.16 2005/08/07 10:02:41 k Exp $
+#
+
+require 'cgi'
+require 'html/template'
+require 'bio/io/keggapi'
+
+MAX_ID_NUM = 50
+
+
+module BioFetchError
+
+  def print_text_page(str)
+    print "Content-type: text/plain; charset=UTF-8\n\n"
+    puts str
+    exit
+  end
+
+  def error1(db)
+    str = "ERROR 1 Unknown database [#{db}]."
+    print_text_page(str)
+  end
+
+  def error2(style)
+    str = "ERROR 2 Unknown style [#{style}]."
+    print_text_page(str)
+  end
+
+  def error3(format, db)
+    str = "ERROR 3 Format [#{format}] not known for database [#{db}]."
+    print_text_page(str)
+  end
+
+  def error4(entry_id, db)
+    str = "ERROR 4 ID [#{entry_id}] not found in database [#{db}]."
+    print_text_page(str)
+  end
+
+  def error5(count)
+    str = "ERROR 5 Too many IDs [#{count}]. Max [#{MAX_ID_NUM}] allowed."
+    print_text_page(str)
+  end
+
+  def error6(info)
+    str = "ERROR 6 Illegal information request [#{info}]."
+    print_text_page(str)
+  end
+
+end
+
+
+
+module KeggAPI
+
+  include BioFetchError
+
+  def list_databases
+    serv = Bio::KEGG::API.new
+    results = serv.list_databases
+    results.collect {|x| x.entry_id}
+  end
+
+  def bget(db, id_list, format)
+    serv = Bio::KEGG::API.new
+    results = ''
+    id_list.each do |query_id|
+      entry_id = "#{db}:#{query_id}"
+      result = serv.get_entries([entry_id])
+      if result.empty?
+        error4(query_id, db)
+      else
+        results << result
+      end
+    end
+    return results
+  end
+
+end
+
+
+
+
+class BioFetch
+
+  include BioFetchError
+  include KeggAPI
+
+  def initialize(db, id_list, style, format)
+    check_style(style)
+    check_format(format, db)
+    check_number_of_id(id_list.length)
+    check_dbname(db)
+
+    if /html/.match(style)
+      goto_html_style_page(db, id_list, format)
+    end
+
+    entries = bget(db, id_list, format)
+
+    if /fasta/.match(format) and entries
+      entries = convert_to_fasta_format(entries, db)
+    end
+
+    print_text_page(entries)
+  end
+
+  private
+
+  def convert_to_fasta_format(str, db)
+    require 'bio'
+    require 'stringio'
+
+    fasta = Array.new
+
+    entries = StringIO.new(str)
+    Bio::FlatFile.auto(entries) do |ff|
+      ff.each do |entry|
+        seq = nil
+        if entry.respond_to?(:seq)
+          seq = entry.seq
+        elsif entry.respond_to?(:aaseq)
+          seq = entry.aaseq
+        elsif entry.respond_to?(:naseq)
+          seq = entry.naseq
+        end
+        if seq
+          entry_id   = entry.respond_to?(:entry_id)   ? entry.entry_id   : ''
+          definition = entry.respond_to?(:definition) ? entry.definition : ''
+          fasta << seq.to_fasta("#{db}:#{entry_id} #{definition}", 60)
+        end
+      end
+    end
+    return fasta.join
+  end
+
+  def goto_html_style_page(db, id_list, format)
+    url = "http://www.genome.jp/dbget-bin/www_bget"
+    opt = '-f+' if /fasta/.match(format)
+    ids = id_list.join('%2B')
+    print "Location: #{url}?#{opt}#{db}+#{ids}\n\n"
+    exit
+  end
+
+  def check_style(style)
+    error2(style) unless /html|raw/.match(style)
+  end
+
+  def check_format(format, db)
+    error3(format, db) if format && ! /fasta|default/.match(format)
+  end
+
+  def check_number_of_id(num)
+    error5(num) if num > MAX_ID_NUM
+  end
+
+  def check_dbname(db)
+    error1(db) unless list_databases.include?(db)
+  end
+
+end
+
+
+
+class BioFetchInfo
+
+  include BioFetchError
+  include KeggAPI
+
+  def initialize(info, db)
+    @db = db
+    begin
+      send(info)
+    rescue
+      error6(info)
+    end
+  end
+
+  private
+
+  def dbs
+    str = list_databases.sort.join(' ')
+    print_text_page(str)
+  end
+
+  def formats
+    fasta = " fasta" if check_fasta_ok
+    str = "default#{fasta}"
+    print_text_page(str)
+  end
+
+  def maxids
+    str = MAX_ID_NUM.to_s
+    print_text_page(str)
+  end
+
+  def check_fasta_ok
+    # sequence databases supported by Bio::FlatFile.auto
+    /genes|gb|genbank|genpept|rs|refseq|emb|sp|swiss|pir/.match(@db)
+  end
+
+end
+
+
+
+class BioFetchCGI
+
+  def initialize(cgi)
+    @cgi = cgi
+    show_page
+  end
+
+  private
+
+  def show_page
+    if info.empty?
+      if id_list.empty?
+        show_query_page
+      else
+        show_result_page(db, id_list, style, format)
+      end
+    else
+      show_info_page(info, db)
+    end
+  end
+
+  def show_query_page
+    html = HTML::Template.new
+    html.set_html(DATA.read)
+    html.param('max_id_num' => MAX_ID_NUM)
+    @cgi.out do
+      html.output
+    end
+  end
+
+  def show_result_page(db, id_list, style, format)
+    BioFetch.new(db, id_list, style, format)
+  end
+
+  def show_info_page(info, db)
+    BioFetchInfo.new(info, db)
+  end
+
+  def info
+    @cgi['info'].downcase
+  end
+
+  def db
+    @cgi['db'].downcase
+  end
+
+  def id_list
+    @cgi['id'].split(/\W/)		# not only ','
+  end
+
+  def style
+    s = @cgi['style'].downcase
+    return s.empty? ? "html" : s
+  end
+
+  def format
+    f = @cgi['format'].downcase
+    return f.empty? ? "default" : f
+  end
+
+end
+
+
+
+BioFetchCGI.new(CGI.new)
+
+
+
+=begin
+
+This program was created during BioHackathon 2002, Tucson and updated
+in Cape Town :)
+
+Rewrited in 2004 to use KEGG API as the bioruby.org server left from Kyoto
+University (where DBGET runs) and the old version could not run without
+having internally accessible DBGET server.
+
+=end
+
+
+__END__
+
+<HTML>
+<HEAD>
+  <LINK href="http://bioruby.org/img/favicon.png" rel="icon" type="image/png">
+  <LINK href="http://bioruby.org/css/bioruby.css" rel="stylesheet" type="text/css">
+  <TITLE>BioFetch interface to GenomeNet/DBGET</TITLE>
+</HEAD>
+
+<BODY bgcolor="#ffffff">
+
+<H1>
+<IMG src="http://bioruby.org/img/ruby.png" align="middle">
+BioFetch interface to
+<A href="http://www.genome.jp/dbget/">GenomeNet/DBGET</A>
+</H1>
+
+<P>This page allows you to retrieve up to <!var:max_id_num> entries at a time from various up-to-date biological databases.</P>
+
+<HR>
+
+<FORM METHOD="post" ENCTYPE="application/x-www-form-urlencoded" action="biofetch.rb">
+
+<SELECT name="db">
+<OPTION value="genbank">GenBank</OPTION>
+<OPTION value="refseq">RefSeq</OPTION>
+<OPTION value="embl">EMBL</OPTION>
+<OPTION value="swissprot">Swiss-Prot</OPTION>
+<OPTION value="pir">PIR</OPTION>
+<OPTION value="prf">PRF</OPTION>
+<OPTION value="pdb">PDB</OPTION>
+<OPTION value="pdbstr">PDBSTR</OPTION>
+<OPTION value="epd">EPD</OPTION>
+<OPTION value="transfac">TRANSFAC</OPTION>
+<OPTION value="prosite">PROSITE</OPTION>
+<OPTION value="pmd">PMD</OPTION>
+<OPTION value="litdb">LITDB</OPTION>
+<OPTION value="omim">OMIM</OPTION>
+<OPTION value="ligand">KEGG/LIGAND</OPTION>
+<OPTION value="pathway">KEGG/PATHWAY</OPTION>
+<OPTION value="brite">KEGG/BRITE</OPTION>
+<OPTION value="genes">KEGG/GENES</OPTION>
+<OPTION value="genome">KEGG/GENOME</OPTION>
+<OPTION value="linkdb">LinkDB</OPTION>
+<OPTION value="aaindex">AAindex</OPTION>
+</SELECT>
+
+<INPUT name="id" size="40" type="text" maxlength="1000">
+
+<SELECT name="format">
+<OPTION value="default">Default</OPTION>
+<OPTION value="fasta">Fasta</OPTION>
+</SELECT>
+
+<SELECT name="style">
+<OPTION value="raw">Raw</OPTION>
+<OPTION value="html">HTML</OPTION>
+</SELECT>
+
+<INPUT type="submit">
+
+</FORM>
+
+<HR>
+
+<H2>Direct access</H2>
+
+<P>http://bioruby.org/cgi-bin/biofetch.rb?format=(default|fasta|...);style=(html|raw);db=(genbank|embl|...);id=ID[,ID,ID,...]</P>
+<P>(NOTE: the option separator ';' can be '&')</P>
+
+<DL>
+  <DT> <U>format</U> (optional)
+  <DD> default|fasta|...
+
+  <DT> <U>style</U> (required)
+  <DD> html|raw
+
+  <DT> <U>db</U> (required)
+  <DD> genbank|refseq|embl|swissprot|pir|prf|pdb|pdbstr|epd|transfac|prosite|pmd|litdb|omim|ligand|pathway|brite|genes|genome|linkdb|aaindex|...
+
+  <DT> <U>id</U> (required)
+  <DD> comma separated list of IDs
+</DL>
+
+<P>See the <A href="http://obda.open-bio.org/">BioFetch specification</A> for more details.</P>
+
+<H2>Server informations</H2>
+
+<DL>
+  <DT> <A href="?info=dbs">What databases are available?</A>
+  <DD> http://bioruby.org/cgi-bin/biofetch.rb?info=dbs
+
+  <DT> <A href="?info=formats;db=embl">What formats does the database X have?</A>
+  <DD> http://bioruby.org/cgi-bin/biofetch.rb?info=formats;db=embl
+
+  <DT> <A href="?info=maxids">How many entries can be retrieved simultaneously?</A>
+  <DD> http://bioruby.org/cgi-bin/biofetch.rb?info=maxids
+</DL>
+
+<H2>Examples</H2>
+
+<DL>
+  <DT> <A href="?format=default;style=raw;db=genbank;id=AJ617376">gb:AJ617376</A> (default/raw)
+  <DD> http://bioruby.org/cgi-bin/biofetch.rb?format=default;style=raw;db=genbank;id=AJ617376
+
+  <DT> <A href="?format=fasta;style=raw;db=genbank;id=AJ617376">gb:AJ617376</A> (fasta/raw)
+  <DD> http://bioruby.org/cgi-bin/biofetch.rb?format=fasta;style=raw;db=genbank;id=AJ617376
+
+  <DT> <A href="?format=default;style=html;db=genbank;id=AJ617376">gb:AJ617376</A> (default/html)
+  <DD> http://bioruby.org/cgi-bin/biofetch.rb?format=default;style=html;db=genbank;id=AJ617376
+
+  <DT> <A href="?format=default;style=raw;db=genbank;id=AJ617376,AJ617377">gb:AJ617376,AJ617377</A> (default/raw, multiple)
+  <DD> http://bioruby.org/cgi-bin/biofetch.rb?format=default;style=raw;db=genbank;id=AJ617376,AJ617377
+
+  <DT> <A href="?format=default;style=raw;db=embl;id=BUM">embl:BUM</A> (default/raw)
+  <DD> http://bioruby.org/cgi-bin/biofetch.rb?format=default;style=raw;db=embl;id=BUM
+
+  <DT> <A href="?format=default;style=raw;db=swissprot;id=CYC_BOVIN">sp:CYC_BOVIN</A> (default/raw)
+  <DD> http://bioruby.org/cgi-bin/biofetch.rb?format=default;style=raw;db=swissprot;id=CYC_BOVIN
+
+  <DT> <A href="?format=fasta;style=raw;db=swissprot;id=CYC_BOVIN">sp:CYC_BOVIN</A> (fasta/raw)
+  <DD> http://bioruby.org/cgi-bin/biofetch.rb?format=fasta;style=raw;db=swissprot;id=CYC_BOVIN
+
+  <DT> <A href="?format=default;style=raw;db=genes;id=b0015">genes:b0015</A> (default/raw)
+  <DD> http://bioruby.org/cgi-bin/biofetch.rb?format=default;style=raw;db=genes;id=b0015
+
+  <DT> <A href="?format=default;style=raw;db=prosite;id=PS00028">ps:PS00028</A> (default/raw)
+  <DD> http://bioruby.org/cgi-bin/biofetch.rb?format=default;style=raw;db=prosite;id=PS00028
+</DL>
+
+<H2>Errors</H2>
+
+<DL>
+  <DT> <A href="?format=default;style=raw;db=nonexistent;id=AJ617376">Error1</A> sample : DB not found
+  <DD> http://bioruby.org/cgi-bin/biofetch.rb?format=default;style=raw;db=nonexistent;id=AJ617376"
+
+  <DT> <A href="?format=default;style=nonexistent;db=genbank;id=AJ617376">Error2</A> sample : unknown style
+  <DD> http://bioruby.org/cgi-bin/biofetch.rb?format=default;style=nonexistent;db=genbank;id=AJ617376"
+
+  <DT> <A href="?format=nonexistent;style=raw;db=genbank;id=AJ617376">Error3</A> sample : unknown format
+  <DD> http://bioruby.org/cgi-bin/biofetch.rb?format=nonexistent;style=raw;db=genbank;id=AJ617376"
+
+  <DT> <A href="?format=default;style=raw;db=genbank;id=nonexistent">Error4</A> sample : ID not found
+  <DD> http://bioruby.org/cgi-bin/biofetch.rb?format=default;style=raw;db=genbank;id=nonexistent"
+
+  <DT> <A href="?style=raw;db=genes;id=1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51">Error5</A> sample : too many IDs
+  <DD> http://bioruby.org/cgi-bin/biofetch.rb?style=raw;db=genes;id=1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51
+
+  <DT> <A href="?info=nonexistent">Error6</A> sample : unknown info
+  <DD> http://bioruby.org/cgi-bin/biofetch.rb?info=nonexistent"
+</DL>
+
+<H2>Other BioFetch implementations</H2>
+
+<UL>
+  <LI> <A href="http://www.ebi.ac.uk/cgi-bin/dbfetch">dbfetch at EBI</A>
+</UL>
+
+<HR>
+
+<DIV align=right>
+<I>
+staff@Bio<span class="ruby">Ruby</span>.org
+</I>
+<BR>
+<BR>
+<A href="http://bioruby.org/"><IMG border=0 src="/img/banner.gif"></A>
+</DIV>
+
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