comparison sappDocker/rnammer.xml @ 31:957156367442 draft

Uploaded
author jjkoehorst
date Wed, 29 Jun 2016 01:36:58 -0400
parents
children
comparison
equal deleted inserted replaced
30:0a947cb25a3d 31:957156367442
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/target/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>