A new protein linear motif benchmark for multiple sequence alignment software View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2008-04-25

AUTHORS

Emmanuel Perrodou, Claudia Chica, Olivier Poch, Toby J Gibson, Julie D Thompson

ABSTRACT

BackgroundLinear motifs (LMs) are abundant short regulatory sites used for modulating the functions of many eukaryotic proteins. They play important roles in post-translational modification, cell compartment targeting, docking sites for regulatory complex assembly and protein processing and cleavage. Methods for LM detection are now being developed that are strongly dependent on scores for motif conservation in homologous proteins. However, most LMs are found in natively disordered polypeptide segments that evolve rapidly, unhindered by structural constraints on the sequence. These regions of modular proteins are difficult to align using classical multiple sequence alignment programs that are specifically optimised to align the globular domains. As a consequence, poor motif alignment quality is hindering efforts to detect new LMs.ResultsWe have developed a new benchmark, as part of the BAliBASE suite, designed to assess the ability of standard multiple alignment methods to detect and align LMs. The reference alignments are organised into different test sets representing real alignment problems and contain examples of experimentally verified functional motifs, extracted from the Eukaryotic Linear Motif (ELM) database. The benchmark has been used to evaluate and compare a number of multiple alignment programs. With distantly related proteins, the worst alignment program correctly aligns 48% of LMs compared to 73% for the best program. However, the performance of all the programs is adversely affected by the introduction of other sequences containing false positive motifs. The ranking of the alignment programs based on LM alignment quality is similar to that observed when considering full-length protein alignments, however little correlation was observed between LM and overall alignment quality for individual alignment test cases.ConclusionWe have shown that none of the programs currently available is capable of reliably aligning LMs in distantly related sequences and we have highlighted a number of specific problems. The results of the tests suggest possible ways to improve program accuracy for difficult, divergent sequences. More... »

PAGES

213

Identifiers

URI

http://scigraph.springernature.com/pub.10.1186/1471-2105-9-213

DOI

http://dx.doi.org/10.1186/1471-2105-9-213

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1049049028

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/18439277


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/2008/08", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Information and Computing Sciences", 
        "type": "DefinedTerm"
      }, 
      {
        "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/0806", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Information Systems", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Amino Acid Motifs", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Artificial Intelligence", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Pattern Recognition, Automated", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Proteins", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Proteomics", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Quality Control", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Reproducibility of Results", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Sequence Alignment", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Sequence Homology, Amino Acid", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Software Validation", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "User-Computer Interface", 
        "type": "DefinedTerm"
      }
    ], 
    "author": [
      {
        "affiliation": {
          "alternateName": "The Centre National de la Recherche Scientifique (CNRS), UMR7104, F-67400 Illkirch, France; Universit\u00e9 Louis Pasteur, F-67000, Strasbourg, France", 
          "id": "http://www.grid.ac/institutes/grid.11843.3f", 
          "name": [
            "Institut de G\u00e9n\u00e9tique et de Biologie Mol\u00e9culaire et Cellulaire (IGBMC), Department of Structural Biology and Genomics, F-67400, Illkirch, France", 
            "Institut National de la Sant\u00e9 et de la Recherche M\u00e9dicale (INSERM), U596, F-67400, Illkirch, France", 
            "The Centre National de la Recherche Scientifique (CNRS), UMR7104, F-67400 Illkirch, France; Universit\u00e9 Louis Pasteur, F-67000, Strasbourg, France"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Perrodou", 
        "givenName": "Emmanuel", 
        "id": "sg:person.01321004215.98", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01321004215.98"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "European Molecular Biology Laboratory, Meyerhofstra\u00dfe 1, 69012, Heidelberg, Germany", 
          "id": "http://www.grid.ac/institutes/grid.4709.a", 
          "name": [
            "European Molecular Biology Laboratory, Meyerhofstra\u00dfe 1, 69012, Heidelberg, Germany"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Chica", 
        "givenName": "Claudia", 
        "id": "sg:person.01362413027.38", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01362413027.38"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "The Centre National de la Recherche Scientifique (CNRS), UMR7104, F-67400 Illkirch, France; Universit\u00e9 Louis Pasteur, F-67000, Strasbourg, France", 
          "id": "http://www.grid.ac/institutes/grid.11843.3f", 
          "name": [
            "Institut de G\u00e9n\u00e9tique et de Biologie Mol\u00e9culaire et Cellulaire (IGBMC), Department of Structural Biology and Genomics, F-67400, Illkirch, France", 
            "Institut National de la Sant\u00e9 et de la Recherche M\u00e9dicale (INSERM), U596, F-67400, Illkirch, France", 
            "The Centre National de la Recherche Scientifique (CNRS), UMR7104, F-67400 Illkirch, France; Universit\u00e9 Louis Pasteur, F-67000, Strasbourg, France"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Poch", 
        "givenName": "Olivier", 
        "id": "sg:person.01136335261.35", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01136335261.35"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "European Molecular Biology Laboratory, Meyerhofstra\u00dfe 1, 69012, Heidelberg, Germany", 
          "id": "http://www.grid.ac/institutes/grid.4709.a", 
          "name": [
            "European Molecular Biology Laboratory, Meyerhofstra\u00dfe 1, 69012, Heidelberg, Germany"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Gibson", 
        "givenName": "Toby J", 
        "id": "sg:person.01254663627.46", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01254663627.46"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "The Centre National de la Recherche Scientifique (CNRS), UMR7104, F-67400 Illkirch, France; Universit\u00e9 Louis Pasteur, F-67000, Strasbourg, France", 
          "id": "http://www.grid.ac/institutes/grid.11843.3f", 
          "name": [
            "Institut de G\u00e9n\u00e9tique et de Biologie Mol\u00e9culaire et Cellulaire (IGBMC), Department of Structural Biology and Genomics, F-67400, Illkirch, France", 
            "Institut National de la Sant\u00e9 et de la Recherche M\u00e9dicale (INSERM), U596, F-67400, Illkirch, France", 
            "The Centre National de la Recherche Scientifique (CNRS), UMR7104, F-67400 Illkirch, France; Universit\u00e9 Louis Pasteur, F-67000, Strasbourg, France"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Thompson", 
        "givenName": "Julie D", 
        "id": "sg:person.01064436555.29", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01064436555.29"
        ], 
        "type": "Person"
      }
    ], 
    "citation": [
      {
        "id": "sg:pub.10.1186/1471-2105-6-298", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1047546418", 
          "https://doi.org/10.1186/1471-2105-6-298"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/1471-2105-6-66", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1041051270", 
          "https://doi.org/10.1186/1471-2105-6-66"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nature05194", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1051876514", 
          "https://doi.org/10.1038/nature05194"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/1471-2105-7-318", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1016092915", 
          "https://doi.org/10.1186/1471-2105-7-318"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/1471-2105-8-193", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1038058129", 
          "https://doi.org/10.1186/1471-2105-8-193"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nmeth856", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1029696607", 
          "https://doi.org/10.1038/nmeth856"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/1471-2105-9-229", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1028307827", 
          "https://doi.org/10.1186/1471-2105-9-229"
        ], 
        "type": "CreativeWork"
      }
    ], 
    "datePublished": "2008-04-25", 
    "datePublishedReg": "2008-04-25", 
    "description": "BackgroundLinear motifs (LMs) are abundant short regulatory sites used for modulating the functions of many eukaryotic proteins. They play important roles in post-translational modification, cell compartment targeting, docking sites for regulatory complex assembly and protein processing and cleavage. Methods for LM detection are now being developed that are strongly dependent on scores for motif conservation in homologous proteins. However, most LMs are found in natively disordered polypeptide segments that evolve rapidly, unhindered by structural constraints on the sequence. These regions of modular proteins are difficult to align using classical multiple sequence alignment programs that are specifically optimised to align the globular domains. As a consequence, poor motif alignment quality is hindering efforts to detect new LMs.ResultsWe have developed a new benchmark, as part of the BAliBASE suite, designed to assess the ability of standard multiple alignment methods to detect and align LMs. The reference alignments are organised into different test sets representing real alignment problems and contain examples of experimentally verified functional motifs, extracted from the Eukaryotic Linear Motif (ELM) database. The benchmark has been used to evaluate and compare a number of multiple alignment programs. With distantly related proteins, the worst alignment program correctly aligns 48% of LMs compared to 73% for the best program. However, the performance of all the programs is adversely affected by the introduction of other sequences containing false positive motifs. The ranking of the alignment programs based on LM alignment quality is similar to that observed when considering full-length protein alignments, however little correlation was observed between LM and overall alignment quality for individual alignment test cases.ConclusionWe have shown that none of the programs currently available is capable of reliably aligning LMs in distantly related sequences and we have highlighted a number of specific problems. The results of the tests suggest possible ways to improve program accuracy for difficult, divergent sequences.", 
    "genre": "article", 
    "id": "sg:pub.10.1186/1471-2105-9-213", 
    "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": "9"
      }
    ], 
    "keywords": [
      "post-translational modifications", 
      "alignment programs", 
      "eukaryotic proteins", 
      "motif conservation", 
      "modular proteins", 
      "Eukaryotic Linear Motif (ELM) database", 
      "complex assembly", 
      "functional motifs", 
      "protein processing", 
      "homologous proteins", 
      "divergent sequences", 
      "multiple sequence alignment software", 
      "globular domain", 
      "polypeptide segments", 
      "regulatory sites", 
      "protein alignments", 
      "related sequences", 
      "motif databases", 
      "multiple alignment program", 
      "multiple alignment methods", 
      "protein", 
      "sequence alignment software", 
      "motif", 
      "multiple sequence alignment program", 
      "sequence alignment programs", 
      "sequence", 
      "alignment quality", 
      "alignment software", 
      "important role", 
      "reference alignment", 
      "conservation", 
      "sites", 
      "structural constraints", 
      "targeting", 
      "assembly", 
      "cleavage", 
      "little correlation", 
      "domain", 
      "alignment", 
      "role", 
      "alignment method", 
      "LM detection", 
      "modification", 
      "region", 
      "function", 
      "number", 
      "LM", 
      "suite", 
      "ability", 
      "new LMS", 
      "consequences", 
      "segments", 
      "ResultsWe", 
      "program", 
      "part", 
      "efforts", 
      "database", 
      "different test sets", 
      "set", 
      "alignment problem", 
      "results", 
      "introduction", 
      "test set", 
      "correlation", 
      "possible ways", 
      "quality", 
      "processing", 
      "example", 
      "detection", 
      "ConclusionWe", 
      "positive motives", 
      "method", 
      "constraints", 
      "way", 
      "ranking", 
      "new benchmark", 
      "best program", 
      "test", 
      "cases", 
      "software", 
      "specific problems", 
      "test cases", 
      "benchmarks", 
      "problem", 
      "program accuracy", 
      "accuracy", 
      "performance", 
      "scores"
    ], 
    "name": "A new protein linear motif benchmark for multiple sequence alignment software", 
    "pagination": "213", 
    "productId": [
      {
        "name": "dimensions_id", 
        "type": "PropertyValue", 
        "value": [
          "pub.1049049028"
        ]
      }, 
      {
        "name": "doi", 
        "type": "PropertyValue", 
        "value": [
          "10.1186/1471-2105-9-213"
        ]
      }, 
      {
        "name": "pubmed_id", 
        "type": "PropertyValue", 
        "value": [
          "18439277"
        ]
      }
    ], 
    "sameAs": [
      "https://doi.org/10.1186/1471-2105-9-213", 
      "https://app.dimensions.ai/details/publication/pub.1049049028"
    ], 
    "sdDataset": "articles", 
    "sdDatePublished": "2022-09-02T15:52", 
    "sdLicense": "https://scigraph.springernature.com/explorer/license/", 
    "sdPublisher": {
      "name": "Springer Nature - SN SciGraph project", 
      "type": "Organization"
    }, 
    "sdSource": "s3://com-springernature-scigraph/baseset/20220902/entities/gbq_results/article/article_455.jsonl", 
    "type": "ScholarlyArticle", 
    "url": "https://doi.org/10.1186/1471-2105-9-213"
  }
]
 

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.10.1186/1471-2105-9-213'

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

curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1186/1471-2105-9-213'

Turtle is a human-readable linked data format.

curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1186/1471-2105-9-213'

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

curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1186/1471-2105-9-213'


 

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

253 TRIPLES      21 PREDICATES      131 URIs      116 LITERALS      18 BLANK NODES

Subject Predicate Object
1 sg:pub.10.1186/1471-2105-9-213 schema:about N14407df42831416a956526651c8de600
2 N26ebf2211ed94bbfa3e3c9bda306f954
3 N3350c4cdc116415787b338b9f4a9dd64
4 N3da7a53c35214287b45ad1e599b9a38a
5 N641286d4687e4aee8f796afd245688cb
6 N8af7b3f0c85f4642a5faac2643d4b54e
7 N8e124f09cd3b49829feaccb8d1ade931
8 N8fc773491bb64c11b1049184caf10ed0
9 Na8d839904c5640e2aa0d39fefeb31b13
10 Nb646a21fc0104762bab81d029786d665
11 Nbd074df6043f43aa900a8f2f4a24819a
12 anzsrc-for:08
13 anzsrc-for:0806
14 schema:author N62c0444c2de14eae8828e5574a9bbc81
15 schema:citation sg:pub.10.1038/nature05194
16 sg:pub.10.1038/nmeth856
17 sg:pub.10.1186/1471-2105-6-298
18 sg:pub.10.1186/1471-2105-6-66
19 sg:pub.10.1186/1471-2105-7-318
20 sg:pub.10.1186/1471-2105-8-193
21 sg:pub.10.1186/1471-2105-9-229
22 schema:datePublished 2008-04-25
23 schema:datePublishedReg 2008-04-25
24 schema:description BackgroundLinear motifs (LMs) are abundant short regulatory sites used for modulating the functions of many eukaryotic proteins. They play important roles in post-translational modification, cell compartment targeting, docking sites for regulatory complex assembly and protein processing and cleavage. Methods for LM detection are now being developed that are strongly dependent on scores for motif conservation in homologous proteins. However, most LMs are found in natively disordered polypeptide segments that evolve rapidly, unhindered by structural constraints on the sequence. These regions of modular proteins are difficult to align using classical multiple sequence alignment programs that are specifically optimised to align the globular domains. As a consequence, poor motif alignment quality is hindering efforts to detect new LMs.ResultsWe have developed a new benchmark, as part of the BAliBASE suite, designed to assess the ability of standard multiple alignment methods to detect and align LMs. The reference alignments are organised into different test sets representing real alignment problems and contain examples of experimentally verified functional motifs, extracted from the Eukaryotic Linear Motif (ELM) database. The benchmark has been used to evaluate and compare a number of multiple alignment programs. With distantly related proteins, the worst alignment program correctly aligns 48% of LMs compared to 73% for the best program. However, the performance of all the programs is adversely affected by the introduction of other sequences containing false positive motifs. The ranking of the alignment programs based on LM alignment quality is similar to that observed when considering full-length protein alignments, however little correlation was observed between LM and overall alignment quality for individual alignment test cases.ConclusionWe have shown that none of the programs currently available is capable of reliably aligning LMs in distantly related sequences and we have highlighted a number of specific problems. The results of the tests suggest possible ways to improve program accuracy for difficult, divergent sequences.
25 schema:genre article
26 schema:isAccessibleForFree true
27 schema:isPartOf N73913c69e3e74c0fb785d6b2993011f1
28 Ncd5e204485874f7e995dcce858e1fe58
29 sg:journal.1023786
30 schema:keywords ConclusionWe
31 Eukaryotic Linear Motif (ELM) database
32 LM
33 LM detection
34 ResultsWe
35 ability
36 accuracy
37 alignment
38 alignment method
39 alignment problem
40 alignment programs
41 alignment quality
42 alignment software
43 assembly
44 benchmarks
45 best program
46 cases
47 cleavage
48 complex assembly
49 consequences
50 conservation
51 constraints
52 correlation
53 database
54 detection
55 different test sets
56 divergent sequences
57 domain
58 efforts
59 eukaryotic proteins
60 example
61 function
62 functional motifs
63 globular domain
64 homologous proteins
65 important role
66 introduction
67 little correlation
68 method
69 modification
70 modular proteins
71 motif
72 motif conservation
73 motif databases
74 multiple alignment methods
75 multiple alignment program
76 multiple sequence alignment program
77 multiple sequence alignment software
78 new LMS
79 new benchmark
80 number
81 part
82 performance
83 polypeptide segments
84 positive motives
85 possible ways
86 post-translational modifications
87 problem
88 processing
89 program
90 program accuracy
91 protein
92 protein alignments
93 protein processing
94 quality
95 ranking
96 reference alignment
97 region
98 regulatory sites
99 related sequences
100 results
101 role
102 scores
103 segments
104 sequence
105 sequence alignment programs
106 sequence alignment software
107 set
108 sites
109 software
110 specific problems
111 structural constraints
112 suite
113 targeting
114 test
115 test cases
116 test set
117 way
118 schema:name A new protein linear motif benchmark for multiple sequence alignment software
119 schema:pagination 213
120 schema:productId Na3f88e0207f54d0f9a27bf5b4fd5b400
121 Nc40ef62afb834619ad78716537b46742
122 Nf94c244b4cad400f8f04fbe9c30be4a5
123 schema:sameAs https://app.dimensions.ai/details/publication/pub.1049049028
124 https://doi.org/10.1186/1471-2105-9-213
125 schema:sdDatePublished 2022-09-02T15:52
126 schema:sdLicense https://scigraph.springernature.com/explorer/license/
127 schema:sdPublisher N012b4678ba8647508aead1f8a52802d6
128 schema:url https://doi.org/10.1186/1471-2105-9-213
129 sgo:license sg:explorer/license/
130 sgo:sdDataset articles
131 rdf:type schema:ScholarlyArticle
132 N012b4678ba8647508aead1f8a52802d6 schema:name Springer Nature - SN SciGraph project
133 rdf:type schema:Organization
134 N14407df42831416a956526651c8de600 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
135 schema:name Sequence Alignment
136 rdf:type schema:DefinedTerm
137 N26ebf2211ed94bbfa3e3c9bda306f954 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
138 schema:name Pattern Recognition, Automated
139 rdf:type schema:DefinedTerm
140 N3350c4cdc116415787b338b9f4a9dd64 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
141 schema:name Reproducibility of Results
142 rdf:type schema:DefinedTerm
143 N3da13a0e050341ce9eeb79c5f5be0264 rdf:first sg:person.01254663627.46
144 rdf:rest Nee8cbb1c396344e6a1dce96e2fd6165c
145 N3da7a53c35214287b45ad1e599b9a38a schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
146 schema:name Proteins
147 rdf:type schema:DefinedTerm
148 N415cd84636d14bb89628d1f503cad50a rdf:first sg:person.01362413027.38
149 rdf:rest N7a4032197971486fb917bd165d08056c
150 N62c0444c2de14eae8828e5574a9bbc81 rdf:first sg:person.01321004215.98
151 rdf:rest N415cd84636d14bb89628d1f503cad50a
152 N641286d4687e4aee8f796afd245688cb schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
153 schema:name Sequence Homology, Amino Acid
154 rdf:type schema:DefinedTerm
155 N73913c69e3e74c0fb785d6b2993011f1 schema:issueNumber 1
156 rdf:type schema:PublicationIssue
157 N7a4032197971486fb917bd165d08056c rdf:first sg:person.01136335261.35
158 rdf:rest N3da13a0e050341ce9eeb79c5f5be0264
159 N8af7b3f0c85f4642a5faac2643d4b54e schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
160 schema:name Amino Acid Motifs
161 rdf:type schema:DefinedTerm
162 N8e124f09cd3b49829feaccb8d1ade931 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
163 schema:name Quality Control
164 rdf:type schema:DefinedTerm
165 N8fc773491bb64c11b1049184caf10ed0 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
166 schema:name Artificial Intelligence
167 rdf:type schema:DefinedTerm
168 Na3f88e0207f54d0f9a27bf5b4fd5b400 schema:name doi
169 schema:value 10.1186/1471-2105-9-213
170 rdf:type schema:PropertyValue
171 Na8d839904c5640e2aa0d39fefeb31b13 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
172 schema:name Software Validation
173 rdf:type schema:DefinedTerm
174 Nb646a21fc0104762bab81d029786d665 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
175 schema:name Proteomics
176 rdf:type schema:DefinedTerm
177 Nbd074df6043f43aa900a8f2f4a24819a schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
178 schema:name User-Computer Interface
179 rdf:type schema:DefinedTerm
180 Nc40ef62afb834619ad78716537b46742 schema:name dimensions_id
181 schema:value pub.1049049028
182 rdf:type schema:PropertyValue
183 Ncd5e204485874f7e995dcce858e1fe58 schema:volumeNumber 9
184 rdf:type schema:PublicationVolume
185 Nee8cbb1c396344e6a1dce96e2fd6165c rdf:first sg:person.01064436555.29
186 rdf:rest rdf:nil
187 Nf94c244b4cad400f8f04fbe9c30be4a5 schema:name pubmed_id
188 schema:value 18439277
189 rdf:type schema:PropertyValue
190 anzsrc-for:08 schema:inDefinedTermSet anzsrc-for:
191 schema:name Information and Computing Sciences
192 rdf:type schema:DefinedTerm
193 anzsrc-for:0806 schema:inDefinedTermSet anzsrc-for:
194 schema:name Information Systems
195 rdf:type schema:DefinedTerm
196 sg:journal.1023786 schema:issn 1471-2105
197 schema:name BMC Bioinformatics
198 schema:publisher Springer Nature
199 rdf:type schema:Periodical
200 sg:person.01064436555.29 schema:affiliation grid-institutes:grid.11843.3f
201 schema:familyName Thompson
202 schema:givenName Julie D
203 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01064436555.29
204 rdf:type schema:Person
205 sg:person.01136335261.35 schema:affiliation grid-institutes:grid.11843.3f
206 schema:familyName Poch
207 schema:givenName Olivier
208 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01136335261.35
209 rdf:type schema:Person
210 sg:person.01254663627.46 schema:affiliation grid-institutes:grid.4709.a
211 schema:familyName Gibson
212 schema:givenName Toby J
213 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01254663627.46
214 rdf:type schema:Person
215 sg:person.01321004215.98 schema:affiliation grid-institutes:grid.11843.3f
216 schema:familyName Perrodou
217 schema:givenName Emmanuel
218 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01321004215.98
219 rdf:type schema:Person
220 sg:person.01362413027.38 schema:affiliation grid-institutes:grid.4709.a
221 schema:familyName Chica
222 schema:givenName Claudia
223 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01362413027.38
224 rdf:type schema:Person
225 sg:pub.10.1038/nature05194 schema:sameAs https://app.dimensions.ai/details/publication/pub.1051876514
226 https://doi.org/10.1038/nature05194
227 rdf:type schema:CreativeWork
228 sg:pub.10.1038/nmeth856 schema:sameAs https://app.dimensions.ai/details/publication/pub.1029696607
229 https://doi.org/10.1038/nmeth856
230 rdf:type schema:CreativeWork
231 sg:pub.10.1186/1471-2105-6-298 schema:sameAs https://app.dimensions.ai/details/publication/pub.1047546418
232 https://doi.org/10.1186/1471-2105-6-298
233 rdf:type schema:CreativeWork
234 sg:pub.10.1186/1471-2105-6-66 schema:sameAs https://app.dimensions.ai/details/publication/pub.1041051270
235 https://doi.org/10.1186/1471-2105-6-66
236 rdf:type schema:CreativeWork
237 sg:pub.10.1186/1471-2105-7-318 schema:sameAs https://app.dimensions.ai/details/publication/pub.1016092915
238 https://doi.org/10.1186/1471-2105-7-318
239 rdf:type schema:CreativeWork
240 sg:pub.10.1186/1471-2105-8-193 schema:sameAs https://app.dimensions.ai/details/publication/pub.1038058129
241 https://doi.org/10.1186/1471-2105-8-193
242 rdf:type schema:CreativeWork
243 sg:pub.10.1186/1471-2105-9-229 schema:sameAs https://app.dimensions.ai/details/publication/pub.1028307827
244 https://doi.org/10.1186/1471-2105-9-229
245 rdf:type schema:CreativeWork
246 grid-institutes:grid.11843.3f schema:alternateName The Centre National de la Recherche Scientifique (CNRS), UMR7104, F-67400 Illkirch, France; Université Louis Pasteur, F-67000, Strasbourg, France
247 schema:name Institut National de la Santé et de la Recherche Médicale (INSERM), U596, F-67400, Illkirch, France
248 Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Department of Structural Biology and Genomics, F-67400, Illkirch, France
249 The Centre National de la Recherche Scientifique (CNRS), UMR7104, F-67400 Illkirch, France; Université Louis Pasteur, F-67000, Strasbourg, France
250 rdf:type schema:Organization
251 grid-institutes:grid.4709.a schema:alternateName European Molecular Biology Laboratory, Meyerhofstraße 1, 69012, Heidelberg, Germany
252 schema:name European Molecular Biology Laboratory, Meyerhofstraße 1, 69012, Heidelberg, Germany
253 rdf:type schema:Organization
 




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


...