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author jjkoehorst
date Wed, 29 Jun 2016 01:36:58 -0400
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1 <tool id="DCRT" name="CRISPR detection" version="0.1">
2 <description></description>
3 <requirements>
4 <container type="docker">jjkoehorst/sappdocker:CRT</container>
5 </requirements>
6 <command interpreter="docker">java -jar /crt/target/CRT-0.0.1-SNAPSHOT-jar-with-dependencies.jar
7 '-input' '$input' -output '$output' -format TURTLE
8 </command>
9 <inputs>
10 <param name="input" type="data" format="ttl" label="genome ttl file" />
11 </inputs>
12
13 <outputs>
14 <data format="ttl" name="output" label="CRISPR: ${input.name}" />
15 </outputs>
16 <help>
17 CIRSPR prediction using CRT. Requires a converted
18 FASTA/EMBL/GenBank file.
19 </help>
20 <citations>
21 <citation type="bibtex">
22 @article{Bland2007,
23 abstract = {BACKGROUND:
24 Clustered Regularly Interspaced Palindromic Repeats
25 (CRISPRs) are a
26 novel type of direct repeat found in a wide range of
27 bacteria and
28 archaea. CRISPRs are beginning to attract attention
29 because of their
30 proposed mechanism; that is, defending their hosts
31 against invading
32 extrachromosomal elements such as viruses. Existing
33 repeat detection
34 tools do a poor job of identifying CRISPRs due to
35 the presence of
36 unique spacer sequences separating the repeats. In
37 this study, a new
38 tool, CRT, is introduced that rapidly and
39 accurately identifies
40 CRISPRs in large DNA strings, such as genomes
41 and metagenomes.
42 RESULTS: CRT was compared to CRISPR detection tools,
43 Patscan and
44 Pilercr. In terms of correctness, CRT was shown to be
45 very reliable,
46 demonstrating significant improvements over Patscan
47 for measures
48 precision, recall and quality. When compared to Pilercr,
49 CRT showed
50 improved performance for recall and quality. In terms of
51 speed, CRT
52 proved to be a huge improvement over Patscan. Both CRT and
53 Pilercr
54 were comparable in speed, however CRT was faster for genomes
55 containing large numbers of repeats. CONCLUSION: In this paper a new
56 tool was introduced for the automatic detection of CRISPR elements.
57 This tool, CRT, showed some important improvements over current
58 techniques for CRISPR identification. CRT's approach to detecting
59 repetitive sequences is straightforward. It uses a simple sequential
60 scan of a DNA sequence and detects repeats directly without any major
61 conversion or preprocessing of the input. This leads to a program
62 that is easy to describe and understand; yet it is very accurate,
63 fast and memory efficient, being O(n) in space and O(nm/l) in time.},
64 author = {Bland, Charles and Ramsey, Teresa L and Sabree, Fareedah
65 and Lowe, Micheal and Brown, Kyndall and Kyrpides, Nikos C and
66 Hugenholtz, Philip},
67 doi = {10.1186/1471-2105-8-209},
68 file =
69 {:Users/koeho006/Library/Application Support/Mendeley
70 Desktop/Downloaded/Bland et al. - 2007 - CRISPR recognition tool
71 (CRT) a tool for automatic detection of clustered regularly
72 interspaced palindromic repeat.pdf:pdf},
73 isbn = {1471-2105
74 (Electronic)$\backslash$n1471-2105 (Linking)},
75 issn = {14712105},
76 journal = {BMC bioinformatics},
77 mendeley-groups = {VAPP Application
78 note},
79 pages = {209},
80 pmid = {17577412},
81 title = {{CRISPR recognition
82 tool (CRT): a tool for automatic detection of
83 clustered regularly
84 interspaced palindromic repeats.}},
85 volume = {8},
86 year = {2007}
87 }
88 </citation>
89 </citations>
90 </tool>