Sybil: Methods and Software for Multiple Genome Comparison and Visualization View Full Text


Ontology type: schema:Chapter     


Chapter Info

DATE

2007

AUTHORS

Jonathan Crabtree , Samuel V. Angiuoli , Jennifer R. Wortman , Owen R. White

ABSTRACT

With the successful completion of genome sequencing projects for a variety of model organisms, the selection of candidate organisms for future sequencing efforts has been guided increasingly by a desire to enable comparative genomics. This trend has both depended on and encouraged the development of software tools that can elucidate and capitalize on the similarities and differences between genomes. “Sybil,” one such tool, is a primarily web-based software package whose primary goal is to facilitate the analysis and visualization of comparative genome data, with a particular emphasis on protein and gene cluster data. Herein, a two-phase protein clustering algorithm, used to generate protein clusters suitable for analysis through Sybil and a method for creating graphical displays of protein or gene clusters that span multiple genomes are described. When combined, these two relatively simple techniques provide the user of the Sybil software (The Institute for Genomic Research [TIGR] Bioinformatics Department) with a browsable graphical display of his or her “input” genomes, showing which genes are conserved based on the parameters supplied to the protein clustering algorithm. For any given protein cluster the graphical display consists of a local alignment of the genomes in which the clustered genes are located. The genomes are arranged in a vertical stack, as in a multiple alignment, and shaded areas are used to connect genes in the same cluster, thus displaying conservation at the protein level in the context of the underlying genomic sequences. The authors have found this display—and slight variants thereof—useful for a variety of annotation and comparison tasks, ranging from identifying “missed” gene models or single-exon discrepancies between orthologous genes, to finding large or small regions of conserved gene synteny, and investigating the properties of the breakpoints between such regions. More... »

PAGES

93-108

Identifiers

URI

http://scigraph.springernature.com/pub.10.1007/978-1-59745-547-3_6

DOI

http://dx.doi.org/10.1007/978-1-59745-547-3_6

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1002756117

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/18314579


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": "Algorithms", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Cluster Analysis", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Databases, Genetic", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Genomics", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Proteins", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Sequence Alignment", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Software", 
        "type": "DefinedTerm"
      }
    ], 
    "author": [
      {
        "affiliation": {
          "alternateName": "The Institute for Genomic Research, Rockville, MD", 
          "id": "http://www.grid.ac/institutes/grid.469946.0", 
          "name": [
            "The Institute for Genomic Research, Rockville, MD"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Crabtree", 
        "givenName": "Jonathan", 
        "id": "sg:person.01064750006.82", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01064750006.82"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "The Institute for Genomic Research, Rockville, MD", 
          "id": "http://www.grid.ac/institutes/grid.469946.0", 
          "name": [
            "The Institute for Genomic Research, Rockville, MD"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Angiuoli", 
        "givenName": "Samuel V.", 
        "id": "sg:person.01343322453.53", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01343322453.53"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "The Institute for Genomic Research, Rockville, MD", 
          "id": "http://www.grid.ac/institutes/grid.469946.0", 
          "name": [
            "The Institute for Genomic Research, Rockville, MD"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Wortman", 
        "givenName": "Jennifer R.", 
        "id": "sg:person.0670072116.14", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0670072116.14"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "The Institute for Genomic Research, Rockville, MD", 
          "id": "http://www.grid.ac/institutes/grid.469946.0", 
          "name": [
            "The Institute for Genomic Research, Rockville, MD"
          ], 
          "type": "Organization"
        }, 
        "familyName": "White", 
        "givenName": "Owen R.", 
        "id": "sg:person.01021555477.04", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01021555477.04"
        ], 
        "type": "Person"
      }
    ], 
    "datePublished": "2007", 
    "datePublishedReg": "2007-01-01", 
    "description": "With the successful completion of genome sequencing projects for a variety of model organisms, the selection of candidate organisms for future sequencing efforts has been guided increasingly by a desire to enable comparative genomics. This trend has both depended on and encouraged the development of software tools that can elucidate and capitalize on the similarities and differences between genomes. \u201cSybil,\u201d one such tool, is a primarily web-based software package whose primary goal is to facilitate the analysis and visualization of comparative genome data, with a particular emphasis on protein and gene cluster data. Herein, a two-phase protein clustering algorithm, used to generate protein clusters suitable for analysis through Sybil and a method for creating graphical displays of protein or gene clusters that span multiple genomes are described. When combined, these two relatively simple techniques provide the user of the Sybil software (The Institute for Genomic Research [TIGR] Bioinformatics Department) with a browsable graphical display of his or her \u201cinput\u201d genomes, showing which genes are conserved based on the parameters supplied to the protein clustering algorithm. For any given protein cluster the graphical display consists of a local alignment of the genomes in which the clustered genes are located. The genomes are arranged in a vertical stack, as in a multiple alignment, and shaded areas are used to connect genes in the same cluster, thus displaying conservation at the protein level in the context of the underlying genomic sequences. The authors have found this display\u2014and slight variants thereof\u2014useful for a variety of annotation and comparison tasks, ranging from identifying \u201cmissed\u201d gene models or single-exon discrepancies between orthologous genes, to finding large or small regions of conserved gene synteny, and investigating the properties of the breakpoints between such regions.", 
    "editor": [
      {
        "familyName": "Ochs", 
        "givenName": "Michael F.", 
        "type": "Person"
      }
    ], 
    "genre": "chapter", 
    "id": "sg:pub.10.1007/978-1-59745-547-3_6", 
    "inLanguage": "en", 
    "isAccessibleForFree": false, 
    "isPartOf": {
      "isbn": [
        "978-1-58829-734-1", 
        "978-1-59745-547-3"
      ], 
      "name": "Gene Function Analysis", 
      "type": "Book"
    }, 
    "keywords": [
      "protein clusters", 
      "clustering algorithm", 
      "future sequencing efforts", 
      "comparative genome data", 
      "graphical display", 
      "genome sequencing projects", 
      "multiple genome comparison", 
      "variety of annotations", 
      "web-based software package", 
      "gene synteny", 
      "orthologous genes", 
      "comparative genomics", 
      "model organisms", 
      "genome comparison", 
      "sequencing efforts", 
      "gene cluster", 
      "gene models", 
      "sequencing projects", 
      "genome data", 
      "genomic sequences", 
      "multiple genomes", 
      "candidate organism", 
      "genome", 
      "software tools", 
      "multiple alignment", 
      "genes", 
      "local alignment", 
      "such tools", 
      "software package", 
      "protein levels", 
      "Sybil", 
      "same cluster", 
      "organisms", 
      "protein", 
      "cluster data", 
      "software", 
      "algorithm", 
      "slight variant", 
      "synteny", 
      "visualization", 
      "genomics", 
      "display", 
      "users", 
      "conservation", 
      "annotation", 
      "tool", 
      "small region", 
      "clusters", 
      "such regions", 
      "sequence", 
      "task", 
      "primary goal", 
      "region", 
      "breakpoints", 
      "alignment", 
      "variants", 
      "variety", 
      "successful completion", 
      "similarity", 
      "package", 
      "comparison task", 
      "selection", 
      "data", 
      "method", 
      "input", 
      "stack", 
      "project", 
      "goal", 
      "analysis", 
      "particular emphasis", 
      "technique", 
      "simple technique", 
      "context", 
      "development", 
      "model", 
      "efforts", 
      "levels", 
      "Herein", 
      "differences", 
      "authors", 
      "parameters", 
      "area", 
      "comparison", 
      "trends", 
      "emphasis", 
      "completion", 
      "desire", 
      "properties", 
      "vertical stack", 
      "discrepancy"
    ], 
    "name": "Sybil: Methods and Software for Multiple Genome Comparison and Visualization", 
    "pagination": "93-108", 
    "productId": [
      {
        "name": "dimensions_id", 
        "type": "PropertyValue", 
        "value": [
          "pub.1002756117"
        ]
      }, 
      {
        "name": "doi", 
        "type": "PropertyValue", 
        "value": [
          "10.1007/978-1-59745-547-3_6"
        ]
      }, 
      {
        "name": "pubmed_id", 
        "type": "PropertyValue", 
        "value": [
          "18314579"
        ]
      }
    ], 
    "publisher": {
      "name": "Springer Nature", 
      "type": "Organisation"
    }, 
    "sameAs": [
      "https://doi.org/10.1007/978-1-59745-547-3_6", 
      "https://app.dimensions.ai/details/publication/pub.1002756117"
    ], 
    "sdDataset": "chapters", 
    "sdDatePublished": "2022-06-01T22:33", 
    "sdLicense": "https://scigraph.springernature.com/explorer/license/", 
    "sdPublisher": {
      "name": "Springer Nature - SN SciGraph project", 
      "type": "Organization"
    }, 
    "sdSource": "s3://com-springernature-scigraph/baseset/20220601/entities/gbq_results/chapter/chapter_343.jsonl", 
    "type": "Chapter", 
    "url": "https://doi.org/10.1007/978-1-59745-547-3_6"
  }
]
 

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.10.1007/978-1-59745-547-3_6'

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

curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1007/978-1-59745-547-3_6'

Turtle is a human-readable linked data format.

curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1007/978-1-59745-547-3_6'

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

curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1007/978-1-59745-547-3_6'


 

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

203 TRIPLES      23 PREDICATES      124 URIs      117 LITERALS      15 BLANK NODES

Subject Predicate Object
1 sg:pub.10.1007/978-1-59745-547-3_6 schema:about N1568e1cf01b84bbbbc5a17db533c87b4
2 N193c3039acab42a1863b70fdd053b98f
3 N2a79da76e2d84fcda056935eb7dc55e5
4 N2c62d8d128b4496e9a9fff2223761aca
5 N7243c9f228804fbd94d3cda33eb9f216
6 N7e6f519d316f4ce88e64027081c86b11
7 Na587782a89e34798baeb04f0e19cec4b
8 anzsrc-for:06
9 anzsrc-for:0604
10 schema:author Nc58df0d1f8d94ab5b1e369a6a0875e29
11 schema:datePublished 2007
12 schema:datePublishedReg 2007-01-01
13 schema:description With the successful completion of genome sequencing projects for a variety of model organisms, the selection of candidate organisms for future sequencing efforts has been guided increasingly by a desire to enable comparative genomics. This trend has both depended on and encouraged the development of software tools that can elucidate and capitalize on the similarities and differences between genomes. “Sybil,” one such tool, is a primarily web-based software package whose primary goal is to facilitate the analysis and visualization of comparative genome data, with a particular emphasis on protein and gene cluster data. Herein, a two-phase protein clustering algorithm, used to generate protein clusters suitable for analysis through Sybil and a method for creating graphical displays of protein or gene clusters that span multiple genomes are described. When combined, these two relatively simple techniques provide the user of the Sybil software (The Institute for Genomic Research [TIGR] Bioinformatics Department) with a browsable graphical display of his or her “input” genomes, showing which genes are conserved based on the parameters supplied to the protein clustering algorithm. For any given protein cluster the graphical display consists of a local alignment of the genomes in which the clustered genes are located. The genomes are arranged in a vertical stack, as in a multiple alignment, and shaded areas are used to connect genes in the same cluster, thus displaying conservation at the protein level in the context of the underlying genomic sequences. The authors have found this display—and slight variants thereof—useful for a variety of annotation and comparison tasks, ranging from identifying “missed” gene models or single-exon discrepancies between orthologous genes, to finding large or small regions of conserved gene synteny, and investigating the properties of the breakpoints between such regions.
14 schema:editor Nbc3ed7f5af324042a2118b2b660723ee
15 schema:genre chapter
16 schema:inLanguage en
17 schema:isAccessibleForFree false
18 schema:isPartOf N3ab0443a874644659b1fb1750720875a
19 schema:keywords Herein
20 Sybil
21 algorithm
22 alignment
23 analysis
24 annotation
25 area
26 authors
27 breakpoints
28 candidate organism
29 cluster data
30 clustering algorithm
31 clusters
32 comparative genome data
33 comparative genomics
34 comparison
35 comparison task
36 completion
37 conservation
38 context
39 data
40 desire
41 development
42 differences
43 discrepancy
44 display
45 efforts
46 emphasis
47 future sequencing efforts
48 gene cluster
49 gene models
50 gene synteny
51 genes
52 genome
53 genome comparison
54 genome data
55 genome sequencing projects
56 genomic sequences
57 genomics
58 goal
59 graphical display
60 input
61 levels
62 local alignment
63 method
64 model
65 model organisms
66 multiple alignment
67 multiple genome comparison
68 multiple genomes
69 organisms
70 orthologous genes
71 package
72 parameters
73 particular emphasis
74 primary goal
75 project
76 properties
77 protein
78 protein clusters
79 protein levels
80 region
81 same cluster
82 selection
83 sequence
84 sequencing efforts
85 sequencing projects
86 similarity
87 simple technique
88 slight variant
89 small region
90 software
91 software package
92 software tools
93 stack
94 successful completion
95 such regions
96 such tools
97 synteny
98 task
99 technique
100 tool
101 trends
102 users
103 variants
104 variety
105 variety of annotations
106 vertical stack
107 visualization
108 web-based software package
109 schema:name Sybil: Methods and Software for Multiple Genome Comparison and Visualization
110 schema:pagination 93-108
111 schema:productId N3ddbd3ee049448daadf822f1ce3caab9
112 N7bef28631f37465486f39ae2fcb27a1c
113 Nfa69f267aece47049dc0a8710cc29030
114 schema:publisher Ne7fdc7ddb310492599008cffb26dd20b
115 schema:sameAs https://app.dimensions.ai/details/publication/pub.1002756117
116 https://doi.org/10.1007/978-1-59745-547-3_6
117 schema:sdDatePublished 2022-06-01T22:33
118 schema:sdLicense https://scigraph.springernature.com/explorer/license/
119 schema:sdPublisher Nf66b00cd1aad4326902987cedd426479
120 schema:url https://doi.org/10.1007/978-1-59745-547-3_6
121 sgo:license sg:explorer/license/
122 sgo:sdDataset chapters
123 rdf:type schema:Chapter
124 N1568e1cf01b84bbbbc5a17db533c87b4 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
125 schema:name Databases, Genetic
126 rdf:type schema:DefinedTerm
127 N193c3039acab42a1863b70fdd053b98f schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
128 schema:name Software
129 rdf:type schema:DefinedTerm
130 N2a79da76e2d84fcda056935eb7dc55e5 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
131 schema:name Cluster Analysis
132 rdf:type schema:DefinedTerm
133 N2c62d8d128b4496e9a9fff2223761aca schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
134 schema:name Proteins
135 rdf:type schema:DefinedTerm
136 N3a09801327254bc9b2eb905b189f6692 rdf:first sg:person.01021555477.04
137 rdf:rest rdf:nil
138 N3ab0443a874644659b1fb1750720875a schema:isbn 978-1-58829-734-1
139 978-1-59745-547-3
140 schema:name Gene Function Analysis
141 rdf:type schema:Book
142 N3ddbd3ee049448daadf822f1ce3caab9 schema:name dimensions_id
143 schema:value pub.1002756117
144 rdf:type schema:PropertyValue
145 N70cceea0007749bf8605a9562de955b1 rdf:first sg:person.0670072116.14
146 rdf:rest N3a09801327254bc9b2eb905b189f6692
147 N7243c9f228804fbd94d3cda33eb9f216 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
148 schema:name Algorithms
149 rdf:type schema:DefinedTerm
150 N7bef28631f37465486f39ae2fcb27a1c schema:name doi
151 schema:value 10.1007/978-1-59745-547-3_6
152 rdf:type schema:PropertyValue
153 N7e6f519d316f4ce88e64027081c86b11 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
154 schema:name Sequence Alignment
155 rdf:type schema:DefinedTerm
156 Na587782a89e34798baeb04f0e19cec4b schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
157 schema:name Genomics
158 rdf:type schema:DefinedTerm
159 Nb6e807f7a1ea46adae65ce4909a0810d rdf:first sg:person.01343322453.53
160 rdf:rest N70cceea0007749bf8605a9562de955b1
161 Nbc3ed7f5af324042a2118b2b660723ee rdf:first Ne5a869075c294df08d63c6600850a4ab
162 rdf:rest rdf:nil
163 Nc58df0d1f8d94ab5b1e369a6a0875e29 rdf:first sg:person.01064750006.82
164 rdf:rest Nb6e807f7a1ea46adae65ce4909a0810d
165 Ne5a869075c294df08d63c6600850a4ab schema:familyName Ochs
166 schema:givenName Michael F.
167 rdf:type schema:Person
168 Ne7fdc7ddb310492599008cffb26dd20b schema:name Springer Nature
169 rdf:type schema:Organisation
170 Nf66b00cd1aad4326902987cedd426479 schema:name Springer Nature - SN SciGraph project
171 rdf:type schema:Organization
172 Nfa69f267aece47049dc0a8710cc29030 schema:name pubmed_id
173 schema:value 18314579
174 rdf:type schema:PropertyValue
175 anzsrc-for:06 schema:inDefinedTermSet anzsrc-for:
176 schema:name Biological Sciences
177 rdf:type schema:DefinedTerm
178 anzsrc-for:0604 schema:inDefinedTermSet anzsrc-for:
179 schema:name Genetics
180 rdf:type schema:DefinedTerm
181 sg:person.01021555477.04 schema:affiliation grid-institutes:grid.469946.0
182 schema:familyName White
183 schema:givenName Owen R.
184 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01021555477.04
185 rdf:type schema:Person
186 sg:person.01064750006.82 schema:affiliation grid-institutes:grid.469946.0
187 schema:familyName Crabtree
188 schema:givenName Jonathan
189 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01064750006.82
190 rdf:type schema:Person
191 sg:person.01343322453.53 schema:affiliation grid-institutes:grid.469946.0
192 schema:familyName Angiuoli
193 schema:givenName Samuel V.
194 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01343322453.53
195 rdf:type schema:Person
196 sg:person.0670072116.14 schema:affiliation grid-institutes:grid.469946.0
197 schema:familyName Wortman
198 schema:givenName Jennifer R.
199 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0670072116.14
200 rdf:type schema:Person
201 grid-institutes:grid.469946.0 schema:alternateName The Institute for Genomic Research, Rockville, MD
202 schema:name The Institute for Genomic Research, Rockville, MD
203 rdf:type schema:Organization
 




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


...