Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) for the Genotyping of Bacterial Pathogens View Full Text


Ontology type: schema:Chapter     


Chapter Info

DATE

2009-03-16

AUTHORS

Ibtissem Grissa , Gilles Vergnaud , Christine Pourcel

ABSTRACT

Clustered regularly interspaced short palindromic repeats (CRISPRs) are DNA sequences composed of a succession of repeats (23- to 47-bp long) separated by unique sequences called spacers. Polymorphism can be observed in different strains of a species and may be used for genotyping. We describe protocols and bioinformatics tools that allow the identification of CRISPRs from sequenced genomes, their comparison, and their component determination (the direct repeats and the spacers). A schematic representation of the spacer organization can be produced, allowing an easy comparison between strains. More... »

PAGES

105-116

Identifiers

URI

http://scigraph.springernature.com/pub.10.1007/978-1-60327-999-4_9

DOI

http://dx.doi.org/10.1007/978-1-60327-999-4_9

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1030694575

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/19521870


Indexing Status Check whether this publication has been indexed by Scopus and Web Of Science using the SN Indexing Status Tool
Incoming Citations Browse incoming citations for this publication using opencitations.net

JSON-LD is the canonical representation for SciGraph data.

TIP: You can open this SciGraph record using an external JSON-LD service: JSON-LD Playground Google SDTT

[
  {
    "@context": "https://springernature.github.io/scigraph/jsonld/sgcontext.json", 
    "about": [
      {
        "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/06", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Biological Sciences", 
        "type": "DefinedTerm"
      }, 
      {
        "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/0604", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Genetics", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Bacteria", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Base Sequence", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "DNA, Bacterial", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Databases, Nucleic Acid", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Genetics, Microbial", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Genome, Bacterial", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Genotype", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Humans", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Inverted Repeat Sequences", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Molecular Epidemiology", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Polymerase Chain Reaction", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Polymorphism, Genetic", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Species Specificity", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Yersinia pestis", 
        "type": "DefinedTerm"
      }
    ], 
    "author": [
      {
        "affiliation": {
          "alternateName": "Department of Genetics and Microbiology, University of Paris XI, Orsay, France", 
          "id": "http://www.grid.ac/institutes/grid.5842.b", 
          "name": [
            "Department of Genetics and Microbiology, University of Paris XI, Orsay, France"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Grissa", 
        "givenName": "Ibtissem", 
        "id": "sg:person.0742060201.14", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0742060201.14"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Department of Genetics and Microbiology, University of Paris XI, Orsay, France", 
          "id": "http://www.grid.ac/institutes/grid.5842.b", 
          "name": [
            "Department of Genetics and Microbiology, University of Paris XI, Orsay, France"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Vergnaud", 
        "givenName": "Gilles", 
        "id": "sg:person.01366533021.19", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01366533021.19"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Department of Genetics and Microbiology, University of Paris XI, Orsay, France", 
          "id": "http://www.grid.ac/institutes/grid.5842.b", 
          "name": [
            "Department of Genetics and Microbiology, University of Paris XI, Orsay, France"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Pourcel", 
        "givenName": "Christine", 
        "id": "sg:person.01021627421.49", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01021627421.49"
        ], 
        "type": "Person"
      }
    ], 
    "datePublished": "2009-03-16", 
    "datePublishedReg": "2009-03-16", 
    "description": "Clustered regularly interspaced short palindromic repeats (CRISPRs) are DNA sequences composed of a succession of repeats (23- to 47-bp long) separated by unique sequences called spacers. Polymorphism can be observed in different strains of a species and may be used for genotyping. We describe protocols and bioinformatics tools that allow the identification of CRISPRs from sequenced genomes, their comparison, and their component determination (the direct repeats and the spacers). A schematic representation of the spacer organization can be produced, allowing an easy comparison between strains.", 
    "editor": [
      {
        "familyName": "Caugant", 
        "givenName": "Dominique A.", 
        "type": "Person"
      }
    ], 
    "genre": "chapter", 
    "id": "sg:pub.10.1007/978-1-60327-999-4_9", 
    "inLanguage": "en", 
    "isAccessibleForFree": false, 
    "isPartOf": {
      "isbn": [
        "978-1-60327-998-7", 
        "978-1-60327-999-4"
      ], 
      "name": "Molecular Epidemiology of Microorganisms", 
      "type": "Book"
    }, 
    "keywords": [
      "short palindromic repeats", 
      "palindromic repeats", 
      "identification of CRISPRs", 
      "spacer organization", 
      "DNA sequences", 
      "unique sequences", 
      "bioinformatics tools", 
      "bacterial pathogens", 
      "repeats", 
      "different strains", 
      "sequence", 
      "genome", 
      "CRISPR", 
      "strains", 
      "species", 
      "pathogens", 
      "polymorphism", 
      "genotyping", 
      "succession", 
      "identification", 
      "spacer", 
      "schematic representation", 
      "organization", 
      "easy comparison", 
      "comparison", 
      "tool", 
      "component determination", 
      "protocol", 
      "determination", 
      "representation", 
      "succession of repeats"
    ], 
    "name": "Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) for the Genotyping of Bacterial Pathogens", 
    "pagination": "105-116", 
    "productId": [
      {
        "name": "dimensions_id", 
        "type": "PropertyValue", 
        "value": [
          "pub.1030694575"
        ]
      }, 
      {
        "name": "doi", 
        "type": "PropertyValue", 
        "value": [
          "10.1007/978-1-60327-999-4_9"
        ]
      }, 
      {
        "name": "pubmed_id", 
        "type": "PropertyValue", 
        "value": [
          "19521870"
        ]
      }
    ], 
    "publisher": {
      "name": "Springer Nature", 
      "type": "Organisation"
    }, 
    "sameAs": [
      "https://doi.org/10.1007/978-1-60327-999-4_9", 
      "https://app.dimensions.ai/details/publication/pub.1030694575"
    ], 
    "sdDataset": "chapters", 
    "sdDatePublished": "2021-12-01T19:58", 
    "sdLicense": "https://scigraph.springernature.com/explorer/license/", 
    "sdPublisher": {
      "name": "Springer Nature - SN SciGraph project", 
      "type": "Organization"
    }, 
    "sdSource": "s3://com-springernature-scigraph/baseset/20211201/entities/gbq_results/chapter/chapter_171.jsonl", 
    "type": "Chapter", 
    "url": "https://doi.org/10.1007/978-1-60327-999-4_9"
  }
]
 

Download the RDF metadata as:  json-ld nt turtle xml License info

HOW TO GET THIS DATA PROGRAMMATICALLY:

JSON-LD is a popular format for linked data which is fully compatible with JSON.

curl -H 'Accept: application/ld+json' 'https://scigraph.springernature.com/pub.10.1007/978-1-60327-999-4_9'

N-Triples is a line-based linked data format ideal for batch operations.

curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1007/978-1-60327-999-4_9'

Turtle is a human-readable linked data format.

curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1007/978-1-60327-999-4_9'

RDF/XML is a standard XML format for linked data.

curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1007/978-1-60327-999-4_9'


 

This table displays all metadata directly associated to this object as RDF triples.

165 TRIPLES      23 PREDICATES      71 URIs      64 LITERALS      22 BLANK NODES

Subject Predicate Object
1 sg:pub.10.1007/978-1-60327-999-4_9 schema:about N1cfed9d3cc2c4612af47f263e742b7a3
2 N22d2c640ff4d4c3c8e6c4a3eadc558f2
3 N36a68222e49b495489aac0f83ab8544e
4 N6647fc01c60f4fc68354fcd0b0121905
5 N68179a6bf7524c28b680fcd7593a8069
6 N72c06e626cee488ab9d07b80945a7c26
7 N91286221df1d48c5904be7d13a235699
8 N92cb701db55042f8a44d4a5ca0a7417e
9 Nb470240ec0d54f0f8d50672c81c3c638
10 Nb4e233aac391427ab5b9b2cd8f3ce814
11 Nb96d32bec259412fadd1c2c30372f112
12 Nc61772dbc234440aaa5ac1a0d9f18ca6
13 Nce89f77a06494708866d97a66d631779
14 Ne0ac500f06884e2e821ce1b5dd819162
15 anzsrc-for:06
16 anzsrc-for:0604
17 schema:author N86f22c3cbcd84392aeddf02dcd056d6f
18 schema:datePublished 2009-03-16
19 schema:datePublishedReg 2009-03-16
20 schema:description Clustered regularly interspaced short palindromic repeats (CRISPRs) are DNA sequences composed of a succession of repeats (23- to 47-bp long) separated by unique sequences called spacers. Polymorphism can be observed in different strains of a species and may be used for genotyping. We describe protocols and bioinformatics tools that allow the identification of CRISPRs from sequenced genomes, their comparison, and their component determination (the direct repeats and the spacers). A schematic representation of the spacer organization can be produced, allowing an easy comparison between strains.
21 schema:editor Nfb018dce13e641e194c3007279bcacfc
22 schema:genre chapter
23 schema:inLanguage en
24 schema:isAccessibleForFree false
25 schema:isPartOf N2023bef3b2be4a508d3b10a8a827a4d9
26 schema:keywords CRISPR
27 DNA sequences
28 bacterial pathogens
29 bioinformatics tools
30 comparison
31 component determination
32 determination
33 different strains
34 easy comparison
35 genome
36 genotyping
37 identification
38 identification of CRISPRs
39 organization
40 palindromic repeats
41 pathogens
42 polymorphism
43 protocol
44 repeats
45 representation
46 schematic representation
47 sequence
48 short palindromic repeats
49 spacer
50 spacer organization
51 species
52 strains
53 succession
54 succession of repeats
55 tool
56 unique sequences
57 schema:name Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) for the Genotyping of Bacterial Pathogens
58 schema:pagination 105-116
59 schema:productId N230ea499a18e4762a843938b5d767ba8
60 N829b43401a0f4db9a959a25907f2ed7c
61 Ndaaa932fa0a04849872627f14d2e571b
62 schema:publisher N466bec8ec33e44f5be6704fee9e41ca1
63 schema:sameAs https://app.dimensions.ai/details/publication/pub.1030694575
64 https://doi.org/10.1007/978-1-60327-999-4_9
65 schema:sdDatePublished 2021-12-01T19:58
66 schema:sdLicense https://scigraph.springernature.com/explorer/license/
67 schema:sdPublisher N0a09c11374a54c7eab47dd87123579fd
68 schema:url https://doi.org/10.1007/978-1-60327-999-4_9
69 sgo:license sg:explorer/license/
70 sgo:sdDataset chapters
71 rdf:type schema:Chapter
72 N0a09c11374a54c7eab47dd87123579fd schema:name Springer Nature - SN SciGraph project
73 rdf:type schema:Organization
74 N1cfed9d3cc2c4612af47f263e742b7a3 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
75 schema:name Yersinia pestis
76 rdf:type schema:DefinedTerm
77 N2023bef3b2be4a508d3b10a8a827a4d9 schema:isbn 978-1-60327-998-7
78 978-1-60327-999-4
79 schema:name Molecular Epidemiology of Microorganisms
80 rdf:type schema:Book
81 N22d2c640ff4d4c3c8e6c4a3eadc558f2 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
82 schema:name Genome, Bacterial
83 rdf:type schema:DefinedTerm
84 N230ea499a18e4762a843938b5d767ba8 schema:name dimensions_id
85 schema:value pub.1030694575
86 rdf:type schema:PropertyValue
87 N36a68222e49b495489aac0f83ab8544e schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
88 schema:name Molecular Epidemiology
89 rdf:type schema:DefinedTerm
90 N3c844d13d1da4050a2ae502a124227c3 schema:familyName Caugant
91 schema:givenName Dominique A.
92 rdf:type schema:Person
93 N466bec8ec33e44f5be6704fee9e41ca1 schema:name Springer Nature
94 rdf:type schema:Organisation
95 N526f1a0c41b14d0d8c373aa402a7b478 rdf:first sg:person.01021627421.49
96 rdf:rest rdf:nil
97 N6647fc01c60f4fc68354fcd0b0121905 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
98 schema:name Genotype
99 rdf:type schema:DefinedTerm
100 N68179a6bf7524c28b680fcd7593a8069 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
101 schema:name DNA, Bacterial
102 rdf:type schema:DefinedTerm
103 N72c06e626cee488ab9d07b80945a7c26 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
104 schema:name Polymorphism, Genetic
105 rdf:type schema:DefinedTerm
106 N829b43401a0f4db9a959a25907f2ed7c schema:name pubmed_id
107 schema:value 19521870
108 rdf:type schema:PropertyValue
109 N86f22c3cbcd84392aeddf02dcd056d6f rdf:first sg:person.0742060201.14
110 rdf:rest Nd28ff9d5856249bd9ea7fa42cb8f3495
111 N91286221df1d48c5904be7d13a235699 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
112 schema:name Base Sequence
113 rdf:type schema:DefinedTerm
114 N92cb701db55042f8a44d4a5ca0a7417e schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
115 schema:name Databases, Nucleic Acid
116 rdf:type schema:DefinedTerm
117 Nb470240ec0d54f0f8d50672c81c3c638 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
118 schema:name Species Specificity
119 rdf:type schema:DefinedTerm
120 Nb4e233aac391427ab5b9b2cd8f3ce814 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
121 schema:name Bacteria
122 rdf:type schema:DefinedTerm
123 Nb96d32bec259412fadd1c2c30372f112 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
124 schema:name Inverted Repeat Sequences
125 rdf:type schema:DefinedTerm
126 Nc61772dbc234440aaa5ac1a0d9f18ca6 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
127 schema:name Humans
128 rdf:type schema:DefinedTerm
129 Nce89f77a06494708866d97a66d631779 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
130 schema:name Polymerase Chain Reaction
131 rdf:type schema:DefinedTerm
132 Nd28ff9d5856249bd9ea7fa42cb8f3495 rdf:first sg:person.01366533021.19
133 rdf:rest N526f1a0c41b14d0d8c373aa402a7b478
134 Ndaaa932fa0a04849872627f14d2e571b schema:name doi
135 schema:value 10.1007/978-1-60327-999-4_9
136 rdf:type schema:PropertyValue
137 Ne0ac500f06884e2e821ce1b5dd819162 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
138 schema:name Genetics, Microbial
139 rdf:type schema:DefinedTerm
140 Nfb018dce13e641e194c3007279bcacfc rdf:first N3c844d13d1da4050a2ae502a124227c3
141 rdf:rest rdf:nil
142 anzsrc-for:06 schema:inDefinedTermSet anzsrc-for:
143 schema:name Biological Sciences
144 rdf:type schema:DefinedTerm
145 anzsrc-for:0604 schema:inDefinedTermSet anzsrc-for:
146 schema:name Genetics
147 rdf:type schema:DefinedTerm
148 sg:person.01021627421.49 schema:affiliation grid-institutes:grid.5842.b
149 schema:familyName Pourcel
150 schema:givenName Christine
151 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01021627421.49
152 rdf:type schema:Person
153 sg:person.01366533021.19 schema:affiliation grid-institutes:grid.5842.b
154 schema:familyName Vergnaud
155 schema:givenName Gilles
156 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01366533021.19
157 rdf:type schema:Person
158 sg:person.0742060201.14 schema:affiliation grid-institutes:grid.5842.b
159 schema:familyName Grissa
160 schema:givenName Ibtissem
161 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0742060201.14
162 rdf:type schema:Person
163 grid-institutes:grid.5842.b schema:alternateName Department of Genetics and Microbiology, University of Paris XI, Orsay, France
164 schema:name Department of Genetics and Microbiology, University of Paris XI, Orsay, France
165 rdf:type schema:Organization
 




Preview window. Press ESC to close (or click here)


...