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annotate rnammer.xml @ 35:fa736576c7ed draft

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author jjkoehorst
date Mon, 04 Jul 2016 10:37:59 -0400
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1 <tool id="DRnammer" name="rRNA detection" 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:RNAMMER</container>
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5 </requirements>
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6 <command interpreter="docker">java -jar /rnammer/rnammer-0.0.1-SNAPSHOT-jar-with-dependencies.jar
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7 '-input' '$input' -output '$output' -format TURTLE
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8 </command>
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9 <inputs>
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10 <param format="ttl" label="genome ttl file" name="input" type="data"/>
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11 </inputs>
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12 <outputs>
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13 <data format="ttl" label="RNA: ${input.name}" name="output"/>
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14 </outputs>
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15 <help>Be aware that this can only be used for academic users; other
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16 users are
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17 requested to contact CBS Software Package Manager at
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18 software@cbs.dtu.dk.
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19 We are investigating alternative prediction
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20 applications, please contact
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21 us if you are aware of such method.
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22 </help>
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23 <citations>
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24 <citation type="bibtex">@article{Lagesen2007,
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25 abstract = {The
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26 publication of a complete genome sequence is usually
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27 accompanied by
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28 annotations of its genes. In contrast to protein
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29 coding genes, genes
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30 for ribosomal RNA (rRNA) are often poorly or
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31 inconsistently annotated.
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32 This makes comparative studies based on
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33 rRNA genes difficult. We have
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34 therefore created computational
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35 predictors for the major rRNA species
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36 from all kingdoms of life and
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37 compiled them into a program called
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38 RNAmmer. The program uses hidden
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39 Markov models trained on data from
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40 the 5S ribosomal RNA database and
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41 the European ribosomal RNA database
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42 project. A pre-screening step
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43 makes the method fast with little loss
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44 of sensitivity, enabling the
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45 analysis of a complete bacterial genome
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46 in less than a minute.
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47 Results from running RNAmmer on a large set of
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48 genomes indicate that
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49 the location of rRNAs can be predicted with a
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50 very high level of
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51 accuracy. Novel, unannotated rRNAs are also
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52 predicted in many
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53 genomes. The software as well as the genome analysis
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54 results are
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55 available at the CBS web server.},
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56 author = {Lagesen, Karin
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57 and Hallin, Peter and R\o dland, Einar Andreas and
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58 Staerfeldt,
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59 Hans-Henrik and Rognes, Torbj\o rn and Ussery, David W},
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60 doi =
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61 {10.1093/nar/gkm160},
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62 file = {:Users/koeho006/Library/Application
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63 Support/Mendeley
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64 Desktop/Downloaded/Lagesen et al. - 2007 - RNAmmer
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65 consistent and
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66 rapid annotation of ribosomal RNA genes.pdf:pdf},
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67 issn =
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68 {1362-4962},
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69 journal = {Nucleic acids research},
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70 keywords =
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71 {Computational Biology,Computational Biology: methods,Genes,
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72 rRNA,Genome, Bacterial,Genomics,Genomics: methods,Markov
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73 Chains,Software},
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74 mendeley-groups = {Dump/VAPP Paper,VAPP Application
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75 note},
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76 month = jan,
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77 number = {9},
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78 pages = {3100--8},
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79 pmid = {17452365},
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80 title = {{RNAmmer: consistent and rapid annotation of ribosomal RNA
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81 genes.}},
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82 volume = {35},
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83 year = {2007}
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84 }
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85 </citation>
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86 </citations>
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87 </tool>