Mercurial > repos > jjkoehorst > sapp
comparison rnammer.xml @ 35:fa736576c7ed draft
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| author | jjkoehorst |
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| date | Mon, 04 Jul 2016 10:37:59 -0400 |
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| 34:f2cbf1230026 | 35:fa736576c7ed |
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| 1 <tool id="DRnammer" name="rRNA detection" version="1.0.0"> | |
| 2 <description/> | |
| 3 <requirements> | |
| 4 <container type="docker">jjkoehorst/sappdocker:RNAMMER</container> | |
| 5 </requirements> | |
| 6 <command interpreter="docker">java -jar /rnammer/rnammer-0.0.1-SNAPSHOT-jar-with-dependencies.jar | |
| 7 '-input' '$input' -output '$output' -format TURTLE | |
| 8 </command> | |
| 9 <inputs> | |
| 10 <param format="ttl" label="genome ttl file" name="input" type="data"/> | |
| 11 </inputs> | |
| 12 <outputs> | |
| 13 <data format="ttl" label="RNA: ${input.name}" name="output"/> | |
| 14 </outputs> | |
| 15 <help>Be aware that this can only be used for academic users; other | |
| 16 users are | |
| 17 requested to contact CBS Software Package Manager at | |
| 18 software@cbs.dtu.dk. | |
| 19 We are investigating alternative prediction | |
| 20 applications, please contact | |
| 21 us if you are aware of such method. | |
| 22 </help> | |
| 23 <citations> | |
| 24 <citation type="bibtex">@article{Lagesen2007, | |
| 25 abstract = {The | |
| 26 publication of a complete genome sequence is usually | |
| 27 accompanied by | |
| 28 annotations of its genes. In contrast to protein | |
| 29 coding genes, genes | |
| 30 for ribosomal RNA (rRNA) are often poorly or | |
| 31 inconsistently annotated. | |
| 32 This makes comparative studies based on | |
| 33 rRNA genes difficult. We have | |
| 34 therefore created computational | |
| 35 predictors for the major rRNA species | |
| 36 from all kingdoms of life and | |
| 37 compiled them into a program called | |
| 38 RNAmmer. The program uses hidden | |
| 39 Markov models trained on data from | |
| 40 the 5S ribosomal RNA database and | |
| 41 the European ribosomal RNA database | |
| 42 project. A pre-screening step | |
| 43 makes the method fast with little loss | |
| 44 of sensitivity, enabling the | |
| 45 analysis of a complete bacterial genome | |
| 46 in less than a minute. | |
| 47 Results from running RNAmmer on a large set of | |
| 48 genomes indicate that | |
| 49 the location of rRNAs can be predicted with a | |
| 50 very high level of | |
| 51 accuracy. Novel, unannotated rRNAs are also | |
| 52 predicted in many | |
| 53 genomes. The software as well as the genome analysis | |
| 54 results are | |
| 55 available at the CBS web server.}, | |
| 56 author = {Lagesen, Karin | |
| 57 and Hallin, Peter and R\o dland, Einar Andreas and | |
| 58 Staerfeldt, | |
| 59 Hans-Henrik and Rognes, Torbj\o rn and Ussery, David W}, | |
| 60 doi = | |
| 61 {10.1093/nar/gkm160}, | |
| 62 file = {:Users/koeho006/Library/Application | |
| 63 Support/Mendeley | |
| 64 Desktop/Downloaded/Lagesen et al. - 2007 - RNAmmer | |
| 65 consistent and | |
| 66 rapid annotation of ribosomal RNA genes.pdf:pdf}, | |
| 67 issn = | |
| 68 {1362-4962}, | |
| 69 journal = {Nucleic acids research}, | |
| 70 keywords = | |
| 71 {Computational Biology,Computational Biology: methods,Genes, | |
| 72 rRNA,Genome, Bacterial,Genomics,Genomics: methods,Markov | |
| 73 Chains,Software}, | |
| 74 mendeley-groups = {Dump/VAPP Paper,VAPP Application | |
| 75 note}, | |
| 76 month = jan, | |
| 77 number = {9}, | |
| 78 pages = {3100--8}, | |
| 79 pmid = {17452365}, | |
| 80 title = {{RNAmmer: consistent and rapid annotation of ribosomal RNA | |
| 81 genes.}}, | |
| 82 volume = {35}, | |
| 83 year = {2007} | |
| 84 } | |
| 85 </citation> | |
| 86 </citations> | |
| 87 </tool> |