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author jjkoehorst
date Mon, 04 Jul 2016 10:53:52 -0400
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children
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1 <tool id="DCRT" name="CRISPR detection" version="0.1">
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2 <description></description>
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3 <requirements>
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4 <container type="docker">jjkoehorst/sappdocker:CRT</container>
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5 </requirements>
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6 <command interpreter="docker">java -jar /crt/CRT-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 name="input" type="data" format="ttl" label="genome ttl file" />
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11 </inputs>
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12
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13 <outputs>
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14 <data format="ttl" name="output" label="CRISPR: ${input.name}" />
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15 </outputs>
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16 <help>
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17 CIRSPR prediction using CRT. Requires a converted
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18 FASTA/EMBL/GenBank file.
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19 </help>
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20 <citations>
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21 <citation type="bibtex">
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22 @article{Bland2007,
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23 abstract = {BACKGROUND:
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24 Clustered Regularly Interspaced Palindromic Repeats
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25 (CRISPRs) are a
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26 novel type of direct repeat found in a wide range of
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27 bacteria and
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28 archaea. CRISPRs are beginning to attract attention
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29 because of their
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30 proposed mechanism; that is, defending their hosts
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31 against invading
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32 extrachromosomal elements such as viruses. Existing
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33 repeat detection
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34 tools do a poor job of identifying CRISPRs due to
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35 the presence of
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36 unique spacer sequences separating the repeats. In
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37 this study, a new
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38 tool, CRT, is introduced that rapidly and
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39 accurately identifies
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40 CRISPRs in large DNA strings, such as genomes
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41 and metagenomes.
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42 RESULTS: CRT was compared to CRISPR detection tools,
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43 Patscan and
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44 Pilercr. In terms of correctness, CRT was shown to be
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45 very reliable,
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46 demonstrating significant improvements over Patscan
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47 for measures
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48 precision, recall and quality. When compared to Pilercr,
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49 CRT showed
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50 improved performance for recall and quality. In terms of
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51 speed, CRT
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52 proved to be a huge improvement over Patscan. Both CRT and
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53 Pilercr
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54 were comparable in speed, however CRT was faster for genomes
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55 containing large numbers of repeats. CONCLUSION: In this paper a new
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56 tool was introduced for the automatic detection of CRISPR elements.
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57 This tool, CRT, showed some important improvements over current
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58 techniques for CRISPR identification. CRT's approach to detecting
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59 repetitive sequences is straightforward. It uses a simple sequential
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60 scan of a DNA sequence and detects repeats directly without any major
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61 conversion or preprocessing of the input. This leads to a program
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62 that is easy to describe and understand; yet it is very accurate,
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63 fast and memory efficient, being O(n) in space and O(nm/l) in time.},
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64 author = {Bland, Charles and Ramsey, Teresa L and Sabree, Fareedah
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65 and Lowe, Micheal and Brown, Kyndall and Kyrpides, Nikos C and
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66 Hugenholtz, Philip},
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67 doi = {10.1186/1471-2105-8-209},
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68 file =
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69 {:Users/koeho006/Library/Application Support/Mendeley
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70 Desktop/Downloaded/Bland et al. - 2007 - CRISPR recognition tool
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71 (CRT) a tool for automatic detection of clustered regularly
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72 interspaced palindromic repeat.pdf:pdf},
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73 isbn = {1471-2105
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74 (Electronic)$\backslash$n1471-2105 (Linking)},
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75 issn = {14712105},
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76 journal = {BMC bioinformatics},
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77 mendeley-groups = {VAPP Application
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78 note},
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79 pages = {209},
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80 pmid = {17577412},
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81 title = {{CRISPR recognition
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82 tool (CRT): a tool for automatic detection of
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83 clustered regularly
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84 interspaced palindromic repeats.}},
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85 volume = {8},
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86 year = {2007}
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87 }
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88 </citation>
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89 </citations>
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90 </tool>