Browsing repeats in genomes: Pygram and an application to non-coding region analysis View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2006-10-26

AUTHORS

Patrick Durand, Frédéric Mahé, Anne-Sophie Valin, Jacques Nicolas

ABSTRACT

BACKGROUND: A large number of studies on genome sequences have revealed the major role played by repeated sequences in the structure, function, dynamics and evolution of genomes. In-depth repeat analysis requires specialized methods, including visualization techniques, to achieve optimum exploratory power. RESULTS: This article presents Pygram, a new visualization application for investigating the organization of repeated sequences in complete genome sequences. The application projects data from a repeat index file on the analysed sequences, and by combining this principle with a query system, is capable of locating repeated sequences with specific properties. In short, Pygram provides an efficient, graphical browser for studying repeats. Implementation of the complete configuration is illustrated in an analysis of CRISPR structures in Archaea genomes and the detection of horizontal transfer between Archaea and Viruses. CONCLUSION: By proposing a new visualization environment to analyse repeated sequences, this application aims to increase the efficiency of laboratories involved in investigating repeat organization in single genomes or across several genomes. More... »

PAGES

477-477

Identifiers

URI

http://scigraph.springernature.com/pub.10.1186/1471-2105-7-477

DOI

http://dx.doi.org/10.1186/1471-2105-7-477

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1003899953

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/17067389


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": "Codon", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Genome, Archaeal", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Genome, Viral", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Repetitive Sequences, Nucleic Acid", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Software", 
        "type": "DefinedTerm"
      }
    ], 
    "author": [
      {
        "affiliation": {
          "alternateName": "IRISA/INRIA, Campus de Beaulieu, 35042 Rennes Cedex, France", 
          "id": "http://www.grid.ac/institutes/grid.410368.8", 
          "name": [
            "IRISA/INRIA, Campus de Beaulieu, 35042 Rennes Cedex, France"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Durand", 
        "givenName": "Patrick", 
        "id": "sg:person.01212030201.29", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01212030201.29"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "ECOBIO, CNRS UMR 6553, Campus de Beaulieu, 35042 Rennes Cedex, France", 
          "id": "http://www.grid.ac/institutes/grid.464156.4", 
          "name": [
            "ECOBIO, CNRS UMR 6553, Campus de Beaulieu, 35042 Rennes Cedex, France"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Mah\u00e9", 
        "givenName": "Fr\u00e9d\u00e9ric", 
        "id": "sg:person.0634023736.53", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0634023736.53"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Institut Curie, Dept transfert, Quadrilat\u00e8re historique H\u00f4pital Saint Louis, Porte 13, 1 rue Claude Vellefaux, 75010 Paris, France", 
          "id": "http://www.grid.ac/institutes/grid.418596.7", 
          "name": [
            "IRISA/INRIA, Campus de Beaulieu, 35042 Rennes Cedex, France", 
            "Institut Curie, Dept transfert, Quadrilat\u00e8re historique H\u00f4pital Saint Louis, Porte 13, 1 rue Claude Vellefaux, 75010 Paris, France"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Valin", 
        "givenName": "Anne-Sophie", 
        "id": "sg:person.0602652501.26", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0602652501.26"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "IRISA/INRIA, Campus de Beaulieu, 35042 Rennes Cedex, France", 
          "id": "http://www.grid.ac/institutes/grid.410368.8", 
          "name": [
            "IRISA/INRIA, Campus de Beaulieu, 35042 Rennes Cedex, France"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Nicolas", 
        "givenName": "Jacques", 
        "id": "sg:person.01143715001.20", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01143715001.20"
        ], 
        "type": "Person"
      }
    ], 
    "citation": [
      {
        "id": "sg:pub.10.1038/nature02579", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1023635121", 
          "https://doi.org/10.1038/nature02579"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1007/978-3-540-24698-5_31", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1039656875", 
          "https://doi.org/10.1007/978-3-540-24698-5_31"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/371215a0", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1028852240", 
          "https://doi.org/10.1038/371215a0"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/1471-2164-7-132", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1043773456", 
          "https://doi.org/10.1186/1471-2164-7-132"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1007/3-540-48452-3_11", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1029445734", 
          "https://doi.org/10.1007/3-540-48452-3_11"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1007/s00239-004-0046-3", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1053505023", 
          "https://doi.org/10.1007/s00239-004-0046-3"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nature04696", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1027944303", 
          "https://doi.org/10.1038/nature04696"
        ], 
        "type": "CreativeWork"
      }
    ], 
    "datePublished": "2006-10-26", 
    "datePublishedReg": "2006-10-26", 
    "description": "BACKGROUND: A large number of studies on genome sequences have revealed the major role played by repeated sequences in the structure, function, dynamics and evolution of genomes. In-depth repeat analysis requires specialized methods, including visualization techniques, to achieve optimum exploratory power.\nRESULTS: This article presents Pygram, a new visualization application for investigating the organization of repeated sequences in complete genome sequences. The application projects data from a repeat index file on the analysed sequences, and by combining this principle with a query system, is capable of locating repeated sequences with specific properties. In short, Pygram provides an efficient, graphical browser for studying repeats. Implementation of the complete configuration is illustrated in an analysis of CRISPR structures in Archaea genomes and the detection of horizontal transfer between Archaea and Viruses.\nCONCLUSION: By proposing a new visualization environment to analyse repeated sequences, this application aims to increase the efficiency of laboratories involved in investigating repeat organization in single genomes or across several genomes.", 
    "genre": "article", 
    "id": "sg:pub.10.1186/1471-2105-7-477", 
    "inLanguage": "en", 
    "isAccessibleForFree": true, 
    "isPartOf": [
      {
        "id": "sg:journal.1023786", 
        "issn": [
          "1471-2105"
        ], 
        "name": "BMC Bioinformatics", 
        "publisher": "Springer Nature", 
        "type": "Periodical"
      }, 
      {
        "issueNumber": "1", 
        "type": "PublicationIssue"
      }, 
      {
        "type": "PublicationVolume", 
        "volumeNumber": "7"
      }
    ], 
    "keywords": [
      "specialized methods", 
      "new visualization applications", 
      "exploratory power", 
      "visualization applications", 
      "index file", 
      "query system", 
      "graphical browser", 
      "visualization environment", 
      "visualization techniques", 
      "large number", 
      "evolution of genomes", 
      "applications", 
      "dynamics", 
      "specific properties", 
      "browser", 
      "region analysis", 
      "files", 
      "principles", 
      "complete configuration", 
      "sequence", 
      "structure", 
      "function", 
      "analysis", 
      "technique", 
      "power", 
      "system", 
      "implementation", 
      "CRISPR structure", 
      "environment", 
      "efficiency", 
      "number", 
      "organization", 
      "properties", 
      "configuration", 
      "detection", 
      "evolution", 
      "method", 
      "article", 
      "data", 
      "single genome", 
      "genome sequence", 
      "complete genome sequence", 
      "analysed sequences", 
      "repeated sequences", 
      "transfer", 
      "repeat organization", 
      "study", 
      "major role", 
      "genome", 
      "repeat analysis", 
      "repeats", 
      "archaea", 
      "horizontal transfer", 
      "efficiency of laboratories", 
      "laboratory", 
      "role", 
      "virus", 
      "depth repeat analysis", 
      "optimum exploratory power", 
      "Pygram", 
      "repeat index file", 
      "new visualization environment", 
      "analyse repeated sequences", 
      "non-coding region analysis"
    ], 
    "name": "Browsing repeats in genomes: Pygram and an application to non-coding region analysis", 
    "pagination": "477-477", 
    "productId": [
      {
        "name": "dimensions_id", 
        "type": "PropertyValue", 
        "value": [
          "pub.1003899953"
        ]
      }, 
      {
        "name": "doi", 
        "type": "PropertyValue", 
        "value": [
          "10.1186/1471-2105-7-477"
        ]
      }, 
      {
        "name": "pubmed_id", 
        "type": "PropertyValue", 
        "value": [
          "17067389"
        ]
      }
    ], 
    "sameAs": [
      "https://doi.org/10.1186/1471-2105-7-477", 
      "https://app.dimensions.ai/details/publication/pub.1003899953"
    ], 
    "sdDataset": "articles", 
    "sdDatePublished": "2021-11-01T18:09", 
    "sdLicense": "https://scigraph.springernature.com/explorer/license/", 
    "sdPublisher": {
      "name": "Springer Nature - SN SciGraph project", 
      "type": "Organization"
    }, 
    "sdSource": "s3://com-springernature-scigraph/baseset/20211101/entities/gbq_results/article/article_430.jsonl", 
    "type": "ScholarlyArticle", 
    "url": "https://doi.org/10.1186/1471-2105-7-477"
  }
]
 

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.10.1186/1471-2105-7-477'

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

curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1186/1471-2105-7-477'

Turtle is a human-readable linked data format.

curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1186/1471-2105-7-477'

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

curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1186/1471-2105-7-477'


 

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

201 TRIPLES      22 PREDICATES      101 URIs      86 LITERALS      12 BLANK NODES

Subject Predicate Object
1 sg:pub.10.1186/1471-2105-7-477 schema:about N0c1cd8ef36844e02beb62e505a06ead0
2 N283bebb6a10f49578fb17e9e7c8132d1
3 N47c86df3529041f48f04de72dbd4669c
4 Na97cfed8740146219970ba25196292b0
5 Ncb5b6f15469f42c4b05d6839e5c4bd9e
6 anzsrc-for:06
7 anzsrc-for:0604
8 schema:author N9c786ab9ccb84540837a125b2bcb815c
9 schema:citation sg:pub.10.1007/3-540-48452-3_11
10 sg:pub.10.1007/978-3-540-24698-5_31
11 sg:pub.10.1007/s00239-004-0046-3
12 sg:pub.10.1038/371215a0
13 sg:pub.10.1038/nature02579
14 sg:pub.10.1038/nature04696
15 sg:pub.10.1186/1471-2164-7-132
16 schema:datePublished 2006-10-26
17 schema:datePublishedReg 2006-10-26
18 schema:description BACKGROUND: A large number of studies on genome sequences have revealed the major role played by repeated sequences in the structure, function, dynamics and evolution of genomes. In-depth repeat analysis requires specialized methods, including visualization techniques, to achieve optimum exploratory power. RESULTS: This article presents Pygram, a new visualization application for investigating the organization of repeated sequences in complete genome sequences. The application projects data from a repeat index file on the analysed sequences, and by combining this principle with a query system, is capable of locating repeated sequences with specific properties. In short, Pygram provides an efficient, graphical browser for studying repeats. Implementation of the complete configuration is illustrated in an analysis of CRISPR structures in Archaea genomes and the detection of horizontal transfer between Archaea and Viruses. CONCLUSION: By proposing a new visualization environment to analyse repeated sequences, this application aims to increase the efficiency of laboratories involved in investigating repeat organization in single genomes or across several genomes.
19 schema:genre article
20 schema:inLanguage en
21 schema:isAccessibleForFree true
22 schema:isPartOf N346d195fa87147fbb0405b6e4cbf56d8
23 N4f802db5f61648098437ba8bdf513e81
24 sg:journal.1023786
25 schema:keywords CRISPR structure
26 Pygram
27 analyse repeated sequences
28 analysed sequences
29 analysis
30 applications
31 archaea
32 article
33 browser
34 complete configuration
35 complete genome sequence
36 configuration
37 data
38 depth repeat analysis
39 detection
40 dynamics
41 efficiency
42 efficiency of laboratories
43 environment
44 evolution
45 evolution of genomes
46 exploratory power
47 files
48 function
49 genome
50 genome sequence
51 graphical browser
52 horizontal transfer
53 implementation
54 index file
55 laboratory
56 large number
57 major role
58 method
59 new visualization applications
60 new visualization environment
61 non-coding region analysis
62 number
63 optimum exploratory power
64 organization
65 power
66 principles
67 properties
68 query system
69 region analysis
70 repeat analysis
71 repeat index file
72 repeat organization
73 repeated sequences
74 repeats
75 role
76 sequence
77 single genome
78 specialized methods
79 specific properties
80 structure
81 study
82 system
83 technique
84 transfer
85 virus
86 visualization applications
87 visualization environment
88 visualization techniques
89 schema:name Browsing repeats in genomes: Pygram and an application to non-coding region analysis
90 schema:pagination 477-477
91 schema:productId N1685dc5f9a9946a1a8847680eef05e92
92 N729df56665604ff6ad7c89c49f22788f
93 N893b764c9e5e448482acb7c899a84eb5
94 schema:sameAs https://app.dimensions.ai/details/publication/pub.1003899953
95 https://doi.org/10.1186/1471-2105-7-477
96 schema:sdDatePublished 2021-11-01T18:09
97 schema:sdLicense https://scigraph.springernature.com/explorer/license/
98 schema:sdPublisher N545d46a314f7403882fa2eb68c0531f4
99 schema:url https://doi.org/10.1186/1471-2105-7-477
100 sgo:license sg:explorer/license/
101 sgo:sdDataset articles
102 rdf:type schema:ScholarlyArticle
103 N0c1cd8ef36844e02beb62e505a06ead0 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
104 schema:name Genome, Archaeal
105 rdf:type schema:DefinedTerm
106 N1685dc5f9a9946a1a8847680eef05e92 schema:name doi
107 schema:value 10.1186/1471-2105-7-477
108 rdf:type schema:PropertyValue
109 N283bebb6a10f49578fb17e9e7c8132d1 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
110 schema:name Repetitive Sequences, Nucleic Acid
111 rdf:type schema:DefinedTerm
112 N346d195fa87147fbb0405b6e4cbf56d8 schema:volumeNumber 7
113 rdf:type schema:PublicationVolume
114 N40077285e4d747d49a9cf36e25fcf252 rdf:first sg:person.0602652501.26
115 rdf:rest N6b50d60a6b9e458381e61431bd2ee1d8
116 N47c86df3529041f48f04de72dbd4669c schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
117 schema:name Genome, Viral
118 rdf:type schema:DefinedTerm
119 N4f802db5f61648098437ba8bdf513e81 schema:issueNumber 1
120 rdf:type schema:PublicationIssue
121 N545d46a314f7403882fa2eb68c0531f4 schema:name Springer Nature - SN SciGraph project
122 rdf:type schema:Organization
123 N6b50d60a6b9e458381e61431bd2ee1d8 rdf:first sg:person.01143715001.20
124 rdf:rest rdf:nil
125 N729df56665604ff6ad7c89c49f22788f schema:name pubmed_id
126 schema:value 17067389
127 rdf:type schema:PropertyValue
128 N893b764c9e5e448482acb7c899a84eb5 schema:name dimensions_id
129 schema:value pub.1003899953
130 rdf:type schema:PropertyValue
131 N9c786ab9ccb84540837a125b2bcb815c rdf:first sg:person.01212030201.29
132 rdf:rest Nfc06423b9641483dbbf14bb64df0561a
133 Na97cfed8740146219970ba25196292b0 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
134 schema:name Software
135 rdf:type schema:DefinedTerm
136 Ncb5b6f15469f42c4b05d6839e5c4bd9e schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
137 schema:name Codon
138 rdf:type schema:DefinedTerm
139 Nfc06423b9641483dbbf14bb64df0561a rdf:first sg:person.0634023736.53
140 rdf:rest N40077285e4d747d49a9cf36e25fcf252
141 anzsrc-for:06 schema:inDefinedTermSet anzsrc-for:
142 schema:name Biological Sciences
143 rdf:type schema:DefinedTerm
144 anzsrc-for:0604 schema:inDefinedTermSet anzsrc-for:
145 schema:name Genetics
146 rdf:type schema:DefinedTerm
147 sg:journal.1023786 schema:issn 1471-2105
148 schema:name BMC Bioinformatics
149 schema:publisher Springer Nature
150 rdf:type schema:Periodical
151 sg:person.01143715001.20 schema:affiliation grid-institutes:grid.410368.8
152 schema:familyName Nicolas
153 schema:givenName Jacques
154 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01143715001.20
155 rdf:type schema:Person
156 sg:person.01212030201.29 schema:affiliation grid-institutes:grid.410368.8
157 schema:familyName Durand
158 schema:givenName Patrick
159 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01212030201.29
160 rdf:type schema:Person
161 sg:person.0602652501.26 schema:affiliation grid-institutes:grid.418596.7
162 schema:familyName Valin
163 schema:givenName Anne-Sophie
164 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0602652501.26
165 rdf:type schema:Person
166 sg:person.0634023736.53 schema:affiliation grid-institutes:grid.464156.4
167 schema:familyName Mahé
168 schema:givenName Frédéric
169 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0634023736.53
170 rdf:type schema:Person
171 sg:pub.10.1007/3-540-48452-3_11 schema:sameAs https://app.dimensions.ai/details/publication/pub.1029445734
172 https://doi.org/10.1007/3-540-48452-3_11
173 rdf:type schema:CreativeWork
174 sg:pub.10.1007/978-3-540-24698-5_31 schema:sameAs https://app.dimensions.ai/details/publication/pub.1039656875
175 https://doi.org/10.1007/978-3-540-24698-5_31
176 rdf:type schema:CreativeWork
177 sg:pub.10.1007/s00239-004-0046-3 schema:sameAs https://app.dimensions.ai/details/publication/pub.1053505023
178 https://doi.org/10.1007/s00239-004-0046-3
179 rdf:type schema:CreativeWork
180 sg:pub.10.1038/371215a0 schema:sameAs https://app.dimensions.ai/details/publication/pub.1028852240
181 https://doi.org/10.1038/371215a0
182 rdf:type schema:CreativeWork
183 sg:pub.10.1038/nature02579 schema:sameAs https://app.dimensions.ai/details/publication/pub.1023635121
184 https://doi.org/10.1038/nature02579
185 rdf:type schema:CreativeWork
186 sg:pub.10.1038/nature04696 schema:sameAs https://app.dimensions.ai/details/publication/pub.1027944303
187 https://doi.org/10.1038/nature04696
188 rdf:type schema:CreativeWork
189 sg:pub.10.1186/1471-2164-7-132 schema:sameAs https://app.dimensions.ai/details/publication/pub.1043773456
190 https://doi.org/10.1186/1471-2164-7-132
191 rdf:type schema:CreativeWork
192 grid-institutes:grid.410368.8 schema:alternateName IRISA/INRIA, Campus de Beaulieu, 35042 Rennes Cedex, France
193 schema:name IRISA/INRIA, Campus de Beaulieu, 35042 Rennes Cedex, France
194 rdf:type schema:Organization
195 grid-institutes:grid.418596.7 schema:alternateName Institut Curie, Dept transfert, Quadrilatère historique Hôpital Saint Louis, Porte 13, 1 rue Claude Vellefaux, 75010 Paris, France
196 schema:name IRISA/INRIA, Campus de Beaulieu, 35042 Rennes Cedex, France
197 Institut Curie, Dept transfert, Quadrilatère historique Hôpital Saint Louis, Porte 13, 1 rue Claude Vellefaux, 75010 Paris, France
198 rdf:type schema:Organization
199 grid-institutes:grid.464156.4 schema:alternateName ECOBIO, CNRS UMR 6553, Campus de Beaulieu, 35042 Rennes Cedex, France
200 schema:name ECOBIO, CNRS UMR 6553, Campus de Beaulieu, 35042 Rennes Cedex, France
201 rdf:type schema:Organization
 




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


...