Mercurial > repos > jjkoehorst > sapp
annotate genecaller.xml @ 36:2201c5d61f16 draft default tip
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author | jjkoehorst |
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date | Mon, 04 Jul 2016 10:53:52 -0400 |
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1 <tool id="DGenes" name="Gene prediction" version="1.0.0"> |
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2 <description/> |
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3 <requirements> |
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4 <container type="docker">jjkoehorst/sappdocker:GENECALLER</container> |
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5 </requirements> |
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6 <command interpreter="docker">java -jar /genecaller/genecaller-0.0.1-SNAPSHOT-jar-with-dependencies.jar |
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7 '-runtype' '$runtype' -input $input -output $output -codon $codon -format TURTLE |
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8 </command> |
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9 <inputs> |
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10 <param format="ttl" label="ttl genome file" name="input" type="data"/> |
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11 <param label="codon table selection" name="codon" type="select"> |
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12 <option value="11">The Bacterial, Archaeal and Plant Plastid Code |
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13 (transl_table=11) |
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14 </option> |
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15 <option value="4">The Mold, Protozoan, Coelenterate Mitochondrial |
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16 and Mycoplasma/Spiroplasma Code (transl_table=4) |
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17 </option> |
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18 </param> |
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19 <param label="single or meta genome" name="runtype" type="select"> |
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20 <option value="single">Single genome analysis</option> |
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21 <option value="meta">Metagenome analysis</option> |
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22 </param> |
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23 </inputs> |
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24 <outputs> |
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25 <data format="ttl" label="ORF: ${input.name}" name="output"/> |
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26 </outputs> |
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27 <help>Prodigal gene prediction requires an RDF file from either a |
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28 Genome FASTA or |
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29 Genbank/EMBL format. |
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30 </help> |
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31 <citations> |
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32 <citation type="bibtex">@article{Hyatt2010, |
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33 abstract = {BACKGROUND: The |
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34 quality of automated gene prediction in microbial |
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35 organisms has |
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36 improved steadily over the past decade, but there is |
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37 still room for |
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38 improvement. Increasing the number of correct |
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39 identifications, both of |
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40 genes and of the translation initiation |
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41 sites for each gene, and |
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42 reducing the overall number of false |
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43 positives, are all desirable |
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44 goals. |
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45 |
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46 RESULTS: With our years of experience in manually curating |
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47 genomes for the |
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48 Joint Genome Institute, we developed a new gene |
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49 prediction algorithm |
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50 called Prodigal (PROkaryotic DYnamic programming |
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51 Gene-finding |
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52 ALgorithm). With Prodigal, we focused specifically on the |
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53 three goals |
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54 of improved gene structure prediction, improved |
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55 translation |
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56 initiation site recognition, and reduced false positives. |
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57 We compared |
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58 the results of Prodigal to existing gene-finding methods |
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59 to |
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60 demonstrate that it met each of these objectives. |
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61 |
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62 CONCLUSION: We |
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63 built a fast, lightweight, open source gene prediction program |
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64 called |
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65 Prodigal http://compbio.ornl.gov/prodigal/. Prodigal achieved |
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66 good |
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67 results compared to existing methods, and we believe it will be |
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68 a |
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69 valuable asset to automated microbial annotation pipelines.}, |
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70 author = |
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71 {Hyatt, Doug and Chen, Gwo-Liang and Locascio, Philip F and |
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72 Land, |
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73 Miriam L and Larimer, Frank W and Hauser, Loren J}, |
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74 doi = |
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75 {10.1186/1471-2105-11-119}, |
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76 file = |
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77 {:Users/koeho006/Library/Application Support/Mendeley |
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78 Desktop/Downloaded/Hyatt et al. - 2010 - Prodigal prokaryotic gene |
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79 recognition and translation initiation site identification.pdf:pdf}, |
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80 issn = {1471-2105}, |
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81 journal = {BMC bioinformatics}, |
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82 keywords = |
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83 {Algorithms,Databases, Genetic,Genome, Bacterial,Peptide Chain |
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84 Initiation, Translational,Peptide Chain Initiation, Translational: |
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85 genetics,Prokaryotic Cells,Software}, |
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86 mendeley-groups = {Dump/VAPP |
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87 Paper}, |
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88 month = jan, |
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89 number = {1}, |
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90 pages = {119}, |
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91 pmid = {20211023}, |
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92 title = {{Prodigal: prokaryotic gene recognition and translation |
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93 initiation site identification.}}, |
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94 url = |
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95 {http://www.biomedcentral.com/1471-2105/11/119}, |
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96 volume = {11}, |
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97 year = |
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98 {2010} |
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99 } |
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100 |
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101 </citation> |
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102 </citations> |
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103 </tool> |