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1 <tool id="align_back_trans" name="Thread nucleotides onto a protein alignment (back-translation)" version="0.0.6">
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2 <description>Gives a codon aware alignment</description>
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3 <requirements>
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4 <requirement type="package" version="1.63">biopython</requirement>
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5 <requirement type="python-module">Bio</requirement>
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6 </requirements>
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7 <stdio>
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8 <!-- Anything other than zero is an error -->
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9 <exit_code range="1:" />
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10 <exit_code range=":-1" />
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11 </stdio>
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12 <version_command interpreter="python">align_back_trans.py --version</version_command>
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13 <command interpreter="python">
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14 align_back_trans.py $prot_align.ext "$prot_align" "$nuc_file" "$out_nuc_align" "$table"
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15 </command>
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16 <inputs>
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17 <param name="prot_align" type="data" format="fasta,muscle,clustal" label="Aligned protein file" help="Mutliple sequence file in FASTA, ClustalW or PHYLIP format." />
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18 <param name="table" type="select" label="Genetic code" help="Tables from the NCBI, these determine the start and stop codons">
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19 <option value="1">1. Standard</option>
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20 <option value="2">2. Vertebrate Mitochondrial</option>
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21 <option value="3">3. Yeast Mitochondrial</option>
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22 <option value="4">4. Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma</option>
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23 <option value="5">5. Invertebrate Mitochondrial</option>
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24 <option value="6">6. Ciliate Macronuclear and Dasycladacean</option>
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25 <option value="9">9. Echinoderm Mitochondrial</option>
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26 <option value="10">10. Euplotid Nuclear</option>
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27 <option value="11">11. Bacterial</option>
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28 <option value="12">12. Alternative Yeast Nuclear</option>
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29 <option value="13">13. Ascidian Mitochondrial</option>
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30 <option value="14">14. Flatworm Mitochondrial</option>
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31 <option value="15">15. Blepharisma Macronuclear</option>
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32 <option value="16">16. Chlorophycean Mitochondrial</option>
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33 <option value="21">21. Trematode Mitochondrial</option>
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34 <option value="22">22. Scenedesmus obliquus</option>
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35 <option value="23">23. Thraustochytrium Mitochondrial</option>
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36 <option value="0">Don't check the translation</option>
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37 </param>
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38 <param name="nuc_file" type="data" format="fasta" label="Unaligned nucleotide sequences" help="FASTA format, using same identifiers as your protein alignment" />
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39 </inputs>
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40 <outputs>
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41 <data name="out_nuc_align" format_source="prot_align" metadata_source="prot_align" label="${prot_align.name} (back-translated)"/>
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42 </outputs>
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43 <tests>
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44 <test>
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45 <param name="prot_align" value="demo_prot_align.fasta" />
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46 <param name="nuc_file" value="demo_nucs.fasta" />
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47 <param name="table" value="0" />
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48 <output name="out_nuc_align" file="demo_nuc_align.fasta" />
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49 </test>
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50 <test>
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51 <param name="prot_align" value="demo_prot_align.fasta" />
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52 <param name="nuc_file" value="demo_nucs_trailing_stop.fasta" />
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53 <param name="table" value="11" />
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54 <output name="out_nuc_align" file="demo_nuc_align.fasta" />
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55 </test>
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56 </tests>
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57 <help>
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58 **What it does**
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59
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60 Takes an input file of aligned protein sequences (typically FASTA or Clustal
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61 format), and a matching file of unaligned nucleotide sequences (FASTA format,
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62 using the same identifiers), and threads the nucleotide sequences onto the
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63 protein alignment to produce a codon aware nucleotide alignment - which can
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64 be viewed as a back translation.
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65
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66 If you specify one of the standard NCBI genetic codes (recommended), then the
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67 translation is verified. This will allow fuzzy matching if stop codons in the
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68 protein sequence have been reprented as X, and will allow for a trailing stop
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69 codon present in the nucleotide sequences but not the protein.
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70
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71 Note - the protein and nucleotide sequences must use the same identifers.
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72
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73 Note - If no translation table is specified, the provided nucleotide sequences
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74 should be exactly three times the length of the protein sequences (exluding the gaps).
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75
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76 Note - the nucleotide FASTA file may contain extra sequences not in the
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77 protein alignment, they will be ignored. This can be useful if for example
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78 you have a nucleotide FASTA file containing all the genes in an organism,
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79 while the protein alignment is for a specific gene family.
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80
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81 **Example**
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82
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83 Given this protein alignment in FASTA format::
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84
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85 >Alpha
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86 DEER
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87 >Beta
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88 DE-R
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89 >Gamma
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90 D--R
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91
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92 and this matching unaligned nucleotide FASTA file::
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93
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94 >Alpha
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95 GATGAGGAACGA
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96 >Beta
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97 GATGAGCGU
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98 >Gamma
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99 GATCGG
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100
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101 the tool would return this nucleotide alignment::
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102
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103 >Alpha
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104 GATGAGGAACGA
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105 >Beta
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106 GATGAG---CGU
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107 >Gamma
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108 GAT------CGG
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109
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110 Notice that all the gaps are multiples of three in length.
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111
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112
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113 **Citation**
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114
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115 This tool uses Biopython, so if you use this Galaxy tool in work leading to a
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116 scientific publication please cite the following paper:
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117
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118 Cock et al (2009). Biopython: freely available Python tools for computational
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119 molecular biology and bioinformatics. Bioinformatics 25(11) 1422-3.
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120 http://dx.doi.org/10.1093/bioinformatics/btp163 pmid:19304878.
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121
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122 This tool is available to install into other Galaxy Instances via the Galaxy
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123 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/align_back_trans
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124 </help>
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125 <citations>
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126 <citation type="doi">10.7717/peerj.167</citation>
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127 <citation type="doi">10.1093/bioinformatics/btp163</citation>
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128 </citations>
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129 </tool>
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