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1 <tool id="rbc_rnabob" name="RNABOB" version="2.2.1.0">
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2 <description>Fast Pattern searching for RNA secondary structures</description>
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3 <requirements>
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4 <requirement type="package" version="2.2.1">rnabob</requirement>
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5 </requirements>
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6 <version_command>echo "2.2.1"</version_command>
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7 <command>
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8 <![CDATA[
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9 rnabob
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10 -q
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11 $fancy
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12 $compStrands
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13 $skipOverlapping
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14 $descriptorFile
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15 $sequenceFile > $stdout
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16 ]]>
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17 </command>
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18 <stdio>
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19 <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error" />
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20 <exit_code range=":-1" level="fatal" description="Error occurred. Please check Tool Standard Error" />
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21 </stdio>
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22 <inputs>
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23 <param name="descriptorFile" type="data" format="txt" multiple="false" label="Motif Descriptor File" help="This file contains the description of the motif for which to search"/>
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24 <param name="sequenceFile" type="data" format="fasta" multiple="false" label="Sequence File" help="This file specifies the sequence in which the motif will be searched"/>
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25 <param name="compStrands" type="boolean" truevalue="-c" falsevalue="" checked="false" label="Also search on complementary strands" help="-c : Search both strands of the supplied sequence"/>
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26 <param name="skipOverlapping" type="boolean" truevalue="-s" falsevalue="" checked="false" label="Skip overlapping matches" help="-s : This is a workaround to avoid a problem in the DNABANK, overlapping matches will be ignored"/>
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27 <param name="fancy" type="boolean" checked="false" truevalue="-F" falsevalue="" label="Show Alignments" help="Display full alignments to pattern"/>
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28 </inputs>
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29 <outputs>
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30 <data format="txt" name="stdout" label="${tool.name} on ${on_string}" />
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31 </outputs>
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32 <tests>
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33 <test>
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34 <param name="descriptorFile" value="r17.des" />
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35 <param name="sequenceFile" value="F22B7.fa" />
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36 <param name="compStrands" value="True" />
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37 <param name="skipOverlapping" value="False" />
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38 <param name="fancy" value="False" />
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39 <output name="stdout" file="r17.bob" />
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40 </test>
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41 <test>
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42 <param name="descriptorFile" value="trna.des" />
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43 <param name="sequenceFile" value="F22B7.fa" />
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44 <param name="compStrands" value="True" />
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45 <param name="skipOverlapping" value="False" />
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46 <param name="fancy" value="False" />
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47 <output name="stdout" file="trna.bob" />
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48 </test>
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49 </tests>
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50 <help>
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51 **What RNABOB does**
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52
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53 RNABOB allows searching a sequence database for RNA structural motifs.
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54 The probe motif is specified in a *descriptor* file,
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55 which describes its primary sequence, secondary structure, and tertiary constraints.
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56 The source in its original packaging can be found at http://selab.janelia.org/software/#rnabob.
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57
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58 -----
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59
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60 **Sequence database format**
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61
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62 RNABOB is currently restricted to reading sequence files in FASTA format.
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63 The command line version of RNABOB can also read sequence files in GCG, EMBL, GenBank and other formats.
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64
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65 -----
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66
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67 **Descriptor file syntax**
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68
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69 The descriptor file syntax is fairly powerful, and allows a great deal of freedom for specifying
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70 RNA motifs. The syntax is therefore a bit complicated.
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71
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72 The descriptor file has two parts: a **topology** description and an **explicit** description.
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73
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74 The first non-blank, non-comment line of the file is the topology description. It defines the
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75 order of occurrence of a series of single-stranded, double-stranded and related elements. Each
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76 element must be given a unique name (a number, typically) and must be prefixed with '**s**',
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77 '**h**', or '**r**', indicating single-strand, helical, or a relational element. Helical and
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78 relational elements are paired to other elements, which are suffixed by a prime, **\'**.
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79
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80 For example::
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81
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82 \
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83 h1 s1 h1'
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84
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85 describes a hairpin loop structure with a simple helix and single-stranded loop. If the helix
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86 always contained a non-canonical base pair at one position, the topology coud be described as::
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87
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88 \
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89 h1 r1 h2 s1 h2' r1' h1'
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90
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91 where r1,r1' indicate a correlation, where the sequence r1 constrains the sequence of r1'.
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92 (Helices are a special case of this.)
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93
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94 The remaining non-comment, non-blank lines are explicit descriptions of each element in turn. Each
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95 line contains 3 or 4 fields, separated by tabs or blank space. The first field is the name of the
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96 element, from the topology description. The second field is the number of mismatches allowed in
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97 this element. The third field is the primary sequence constraint to apply to this element.
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98
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99 Helices and relational element pairs are specified on a single line rather than two. Mismatches
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100 and primary sequence constraints are given as pairs, separated by a colon '**:**'. The left side
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101 is the constraint applied to the upstream element, and the right side is applied to the downstream
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102 elements.
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103
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104 The primary sequence constraint is given as a sequence of nucleotides. Any IUPAC single-letter
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105 code is recognized, including N if the position can have any base identity. Allowed length
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106 variations are specified with asterisks ``'*'``, where each ``*`` will allow either 0 or 1 N at
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107 that position.
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108
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109 For example::
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110
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111 \
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112 GGAGG******NNNAUG
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113
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114 specifies a GGAGG Shine/Dalgarno site and an AUG initiation codon, separated by a spacer of 3 to 9
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115 nucleotides of any sequence.
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116
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117 An alternative syntax can be used for very long gaps::
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118
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119 \
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120 GGAGG[10]NNNAUG is the same as GGAGG**********NNNAUG
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121
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122 Be careful defining variable length helices and relational elements; if the number and type (gap
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123 or identity) of position do not match on left and right sides, the program will refuse to accept
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124 the descriptor.
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125
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126 Relational elements have an additional field which specifies a "transformation matrix" of four
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127 nucleotides, specifying the rule for making the ``r'`` pattern from the ``r`` sequence in order
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128 ``A-C-G-T``. For example, the transformation matrix for a simple helix is ``TGCA``; if you allow
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129 ``G-U`` pairs, it is ``TGYR``. RNABOB allows ``G-U`` pairing by default and uses the ``TGYR``
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130 matrix for helical elements.
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131
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132 For example, the explicit description of our hairpin might be:
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133
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134 ::
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135
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136 \
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137 h1 0:0 NNN:NNN
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138 r1 0:0 R:N GNAN
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139 h2 0:0 **NC:GN**
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140 s1 0 UUCG
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141
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142 This describes a stem of 6 to 8 base pairs, in which the 4th pair from the bottom of the stem must
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143 be a non-canonical GA pair. Note that, in general, the left side of the primary constraint for
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144 helices and relational elements is redundant, and should be given as all N. In some cases it is
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145 convenient to constrain the right side to require a particular base pair (GU, for instance) at one
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146 position.
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147
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148 A note on mismatches: The split format for helices and relational elements works like this. The
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149 number on the left constrains the primary sequence match of the left side of the primary
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150 constraint. The number on the right constrains the match of the right side of the primary
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151 constraint, *after* that side has been constructed according to the sequence on the left. In other
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152 words, the number on the left constrains the mismatches in primary sequence only, while the number
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153 on the right will constrain the number of mispaired positions in the helix.
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154
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155 Finally: any line that begins with a pound sign '#' is a comment line, and will not be interpreted
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156 by the pattern compiler.
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157
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158 **Options**
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159
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160 The behavior of RNABOB can be modified by use of the following options:
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161
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162 *Complement*: Selecting this option will cause RNABOB to search for the pattern also on the
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163 complementary strands.
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164
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165 *Skip*: This is a workaround to avoid a problem in the DNABANK. There are some sequences in the
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166 database which have long stretches of ambiguous sequence (N's). Descriptors with no primary
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167 sequence constraints will match these garbage sequences at many, many positions, and generate huge
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168 outputs. This option toggles a search strategy that skips forward a pattern-length rather than a
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169 single base when a match is found, thus printing out only a single match when overlapping matches
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170 are found.
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171
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172 **Examples**
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173
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174 The following example descriptors included in the source distribution
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175 (http://selab.janelia.org/software/rnabob/rnabob.tar.gz):
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176
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177 - trna.des - a general descriptor of a tRNA structure
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178 - r17.des - descriptor of the consensus binding site for the r17 phage coat protein
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179 - pseudoknot.des - description of a simple pseudoknotted structure
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180
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181 An example cosmid ``F22B7.fa`` from the *C. elegans* genome sequencing project is also provided
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182 for running these descriptors against.
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183
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184 ::
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185
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186 \
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187 # trna.des
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188 #
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189 # Generalized descriptor of a tRNA cloverleaf. Doesn't
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190 # find them all though.
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191 #
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192
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193 h1 s1 h2 s2 h2' s3 h3 s4 h3' s5 h4 s6 h4' h1' s8
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194
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195 h1 0:2 NNNNNNN:NNNNNNN
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196 h2 0:1 *NNN:NNN*
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197 h3 0:1 NNNNN:NNNNN
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198 h4 0:1 NNNNN:NNNNN
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199 s1 0 TN
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200 s2 0 NNNN**********
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201 s3 0 N
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202 s4 0 NNNNNN*
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203 s5 0 NN********************
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204 s6 0 TTC****
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205 s8 0 NCCA
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206
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207 Running RNABOB with ``trna.des`` against ``F22B7.fa`` searches the top strand of the cosmid for
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208 the above motif. ``trna.des`` hits twice, once on each strand. (F22B7 has several other tRNA genes
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209 in it which the pattern fails to detect - this is *not* a pattern to use for tRNA genefinding!).
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210 </help>
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211 <citations>
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212 <citation type="doi">10.1093/bioinformatics/6.4.325</citation>
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213 <citation type="bibtex">@UNPUBLISHED{rnabob,
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214 author = {Eddy S.R},
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215 title = {RNABOB: a program to search for RNA secondary structure motifs in sequence databases},
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216 note = {}}</citation>
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217 </citations>
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218 </tool>
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