CloVR-Comparative: automated, cloud-enabled comparative microbial genome sequence analysis pipeline View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2017-12

AUTHORS

Sonia Agrawal, Cesar Arze, Ricky S. Adkins, Jonathan Crabtree, David Riley, Mahesh Vangala, Kevin Galens, Claire M. Fraser, Hervé Tettelin, Owen White, Samuel V. Angiuoli, Anup Mahurkar, W. Florian Fricke

ABSTRACT

BACKGROUND: The benefit of increasing genomic sequence data to the scientific community depends on easy-to-use, scalable bioinformatics support. CloVR-Comparative combines commonly used bioinformatics tools into an intuitive, automated, and cloud-enabled analysis pipeline for comparative microbial genomics. RESULTS: CloVR-Comparative runs on annotated complete or draft genome sequences that are uploaded by the user or selected via a taxonomic tree-based user interface and downloaded from NCBI. CloVR-Comparative runs reference-free multiple whole-genome alignments to determine unique, shared and core coding sequences (CDSs) and single nucleotide polymorphisms (SNPs). Output includes short summary reports and detailed text-based results files, graphical visualizations (phylogenetic trees, circular figures), and a database file linked to the Sybil comparative genome browser. Data up- and download, pipeline configuration and monitoring, and access to Sybil are managed through CloVR-Comparative web interface. CloVR-Comparative and Sybil are distributed as part of the CloVR virtual appliance, which runs on local computers or the Amazon EC2 cloud. Representative datasets (e.g. 40 draft and complete Escherichia coli genomes) are processed in <36 h on a local desktop or at a cost of <$20 on EC2. CONCLUSIONS: CloVR-Comparative allows anybody with Internet access to run comparative genomics projects, while eliminating the need for on-site computational resources and expertise. More... »

PAGES

332

References to SciGraph publications

Identifiers

URI

http://scigraph.springernature.com/pub.10.1186/s12864-017-3717-3

DOI

http://dx.doi.org/10.1186/s12864-017-3717-3

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1084955821

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/28449639


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/2008/0806", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Information Systems", 
        "type": "DefinedTerm"
      }, 
      {
        "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"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Automation", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Cloud Computing", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Genome, Microbial", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Genomics", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Sequence Alignment", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Sequence Analysis", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Software", 
        "type": "DefinedTerm"
      }
    ], 
    "author": [
      {
        "affiliation": {
          "name": [
            "Institute for Genome Sciences, Baltimore, MD, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Agrawal", 
        "givenName": "Sonia", 
        "id": "sg:person.01042442240.45", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01042442240.45"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "name": [
            "Institute for Genome Sciences, Baltimore, MD, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Arze", 
        "givenName": "Cesar", 
        "id": "sg:person.01117132167.66", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01117132167.66"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "name": [
            "Institute for Genome Sciences, Baltimore, MD, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Adkins", 
        "givenName": "Ricky S.", 
        "id": "sg:person.010702355363.91", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.010702355363.91"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "name": [
            "Institute for Genome Sciences, Baltimore, MD, USA"
          ], 
          "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": {
          "name": [
            "Institute for Genome Sciences, Baltimore, MD, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Riley", 
        "givenName": "David", 
        "id": "sg:person.0773431027.21", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0773431027.21"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "name": [
            "Institute for Genome Sciences, Baltimore, MD, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Vangala", 
        "givenName": "Mahesh", 
        "id": "sg:person.01333250544.05", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01333250544.05"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "name": [
            "Institute for Genome Sciences, Baltimore, MD, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Galens", 
        "givenName": "Kevin", 
        "id": "sg:person.01267213104.21", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01267213104.21"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "University of Maryland, Baltimore", 
          "id": "https://www.grid.ac/institutes/grid.411024.2", 
          "name": [
            "Institute for Genome Sciences, Baltimore, MD, USA", 
            "Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Fraser", 
        "givenName": "Claire M.", 
        "id": "sg:person.01123616342.98", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01123616342.98"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "University of Maryland, Baltimore", 
          "id": "https://www.grid.ac/institutes/grid.411024.2", 
          "name": [
            "Institute for Genome Sciences, Baltimore, MD, USA", 
            "Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Tettelin", 
        "givenName": "Herv\u00e9", 
        "id": "sg:person.01065620174.76", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01065620174.76"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "University of Maryland, Baltimore", 
          "id": "https://www.grid.ac/institutes/grid.411024.2", 
          "name": [
            "Institute for Genome Sciences, Baltimore, MD, USA", 
            "Department of Epidemiology, University of Maryland School of Medicine, Baltimore, MD, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "White", 
        "givenName": "Owen", 
        "id": "sg:person.01021555477.04", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01021555477.04"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "name": [
            "Institute for Genome Sciences, Baltimore, MD, USA"
          ], 
          "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": {
          "name": [
            "Institute for Genome Sciences, Baltimore, MD, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Mahurkar", 
        "givenName": "Anup", 
        "id": "sg:person.01051370761.80", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01051370761.80"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "University of Hohenheim", 
          "id": "https://www.grid.ac/institutes/grid.9464.f", 
          "name": [
            "Institute for Genome Sciences, Baltimore, MD, USA", 
            "Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA", 
            "Department of Nutrigenomics, University of Hohenheim, Stuttgart, Germany"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Fricke", 
        "givenName": "W. Florian", 
        "id": "sg:person.01363437654.08", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01363437654.08"
        ], 
        "type": "Person"
      }
    ], 
    "citation": [
      {
        "id": "https://doi.org/10.1371/journal.pone.0009490", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1000778834"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/1471-2105-6-2", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1001691322", 
          "https://doi.org/10.1186/1471-2105-6-2"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/1471-2105-6-2", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1001691322", 
          "https://doi.org/10.1186/1471-2105-6-2"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/bioinformatics/btq665", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1002444689"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1056/nejmoa1106920", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1002495373"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/nar/gku1152", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1008767475"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1128/iai.00932-10", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1010710799"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1056/nejmoa1107643", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1013031508"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.mib.2014.11.004", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1013381248"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/npre.2011.5887.3", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1013539817", 
          "https://doi.org/10.1038/npre.2011.5887.3"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/bioinformatics/btq167", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1015659639"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/nar/gkw255", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1017803216"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1128/aem.00929-12", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1021965475"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/gb-2004-5-2-r12", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1022585853", 
          "https://doi.org/10.1186/gb-2004-5-2-r12"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/nar/gkh340", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1025846396"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/1471-2105-12-356", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1026686709", 
          "https://doi.org/10.1186/1471-2105-12-356"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/nar/gkr1044", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1028349189"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/1471-2105-12-272", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1033419151", 
          "https://doi.org/10.1186/1471-2105-12-272"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/s1473-3099(12)70268-2", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1035688197"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/bioinformatics/btu505", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1036753823"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/bioinformatics/btv689", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1042008257"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1128/mbio.00565-13", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1043224494"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1056/nejmoa1003176", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1043453056"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1007/s00203-011-0725-6", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1046599734", 
          "https://doi.org/10.1007/s00203-011-0725-6"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/bioinformatics/btr652", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1048309275"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/nar/gkp919", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1050742720"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1371/journal.pone.0026624", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1052415595"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1128/jb.00297-11", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1052942562"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1371/journal.pone.0060120", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1053017354"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.4161/gmic.2.1.14911", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1072303866"
        ], 
        "type": "CreativeWork"
      }
    ], 
    "datePublished": "2017-12", 
    "datePublishedReg": "2017-12-01", 
    "description": "BACKGROUND: The benefit of increasing genomic sequence data to the scientific community depends on easy-to-use, scalable bioinformatics support. CloVR-Comparative combines commonly used bioinformatics tools into an intuitive, automated, and cloud-enabled analysis pipeline for comparative microbial genomics.\nRESULTS: CloVR-Comparative runs on annotated complete or draft genome sequences that are uploaded by the user or selected via a taxonomic tree-based user interface and downloaded from NCBI. CloVR-Comparative runs reference-free multiple whole-genome alignments to determine unique, shared and core coding sequences (CDSs) and single nucleotide polymorphisms (SNPs). Output includes short summary reports and detailed text-based results files, graphical visualizations (phylogenetic trees, circular figures), and a database file linked to the Sybil comparative genome browser. Data up- and download, pipeline configuration and monitoring, and access to Sybil are managed through CloVR-Comparative web interface. CloVR-Comparative and Sybil are distributed as part of the CloVR virtual appliance, which runs on local computers or the Amazon EC2 cloud. Representative datasets (e.g. 40 draft and complete Escherichia coli genomes) are processed in <36\u00a0h on a local desktop or at a cost of\u2009<$20 on EC2.\nCONCLUSIONS: CloVR-Comparative allows anybody with Internet access to run comparative genomics projects, while eliminating the need for on-site computational resources and expertise.", 
    "genre": "research_article", 
    "id": "sg:pub.10.1186/s12864-017-3717-3", 
    "inLanguage": [
      "en"
    ], 
    "isAccessibleForFree": true, 
    "isFundedItemOf": [
      {
        "id": "sg:grant.2346893", 
        "type": "MonetaryGrant"
      }
    ], 
    "isPartOf": [
      {
        "id": "sg:journal.1023790", 
        "issn": [
          "1471-2164"
        ], 
        "name": "BMC Genomics", 
        "type": "Periodical"
      }, 
      {
        "issueNumber": "1", 
        "type": "PublicationIssue"
      }, 
      {
        "type": "PublicationVolume", 
        "volumeNumber": "18"
      }
    ], 
    "name": "CloVR-Comparative: automated, cloud-enabled comparative microbial genome sequence analysis pipeline", 
    "pagination": "332", 
    "productId": [
      {
        "name": "readcube_id", 
        "type": "PropertyValue", 
        "value": [
          "40ce8bdfd43044c878c6a9806c3a97a5dca0d801aa5d7e1454188003d5da0e56"
        ]
      }, 
      {
        "name": "pubmed_id", 
        "type": "PropertyValue", 
        "value": [
          "28449639"
        ]
      }, 
      {
        "name": "nlm_unique_id", 
        "type": "PropertyValue", 
        "value": [
          "100965258"
        ]
      }, 
      {
        "name": "doi", 
        "type": "PropertyValue", 
        "value": [
          "10.1186/s12864-017-3717-3"
        ]
      }, 
      {
        "name": "dimensions_id", 
        "type": "PropertyValue", 
        "value": [
          "pub.1084955821"
        ]
      }
    ], 
    "sameAs": [
      "https://doi.org/10.1186/s12864-017-3717-3", 
      "https://app.dimensions.ai/details/publication/pub.1084955821"
    ], 
    "sdDataset": "articles", 
    "sdDatePublished": "2019-04-11T09:41", 
    "sdLicense": "https://scigraph.springernature.com/explorer/license/", 
    "sdPublisher": {
      "name": "Springer Nature - SN SciGraph project", 
      "type": "Organization"
    }, 
    "sdSource": "s3://com-uberresearch-data-dimensions-target-20181106-alternative/cleanup/v134/2549eaecd7973599484d7c17b260dba0a4ecb94b/merge/v9/a6c9fde33151104705d4d7ff012ea9563521a3ce/jats-lookup/v90/0000000346_0000000346/records_99841_00000004.jsonl", 
    "type": "ScholarlyArticle", 
    "url": "https://link.springer.com/10.1186%2Fs12864-017-3717-3"
  }
]
 

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/s12864-017-3717-3'

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/s12864-017-3717-3'

Turtle is a human-readable linked data format.

curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1186/s12864-017-3717-3'

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

curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1186/s12864-017-3717-3'


 

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

300 TRIPLES      21 PREDICATES      65 URIs      28 LITERALS      16 BLANK NODES

Subject Predicate Object
1 sg:pub.10.1186/s12864-017-3717-3 schema:about N0fd64de1f43340509de5407006c65545
2 Na8f4402dbef64e299e0d054436a37ebf
3 Nc13bf5d243214c1d9d081cb67faa5121
4 Nc2cccaa5cd5b4362b9cec53793bb2b16
5 Ndea8e718919a45f5943429090814440c
6 Neb257c8bf6dd4e4e9f4d922e9c9d4ce0
7 Nf6335b01b9db48e19e6d484067df989d
8 anzsrc-for:08
9 anzsrc-for:0806
10 schema:author Nc433b1b2893946c783f559db7cb7399b
11 schema:citation sg:pub.10.1007/s00203-011-0725-6
12 sg:pub.10.1038/npre.2011.5887.3
13 sg:pub.10.1186/1471-2105-12-272
14 sg:pub.10.1186/1471-2105-12-356
15 sg:pub.10.1186/1471-2105-6-2
16 sg:pub.10.1186/gb-2004-5-2-r12
17 https://doi.org/10.1016/j.mib.2014.11.004
18 https://doi.org/10.1016/s1473-3099(12)70268-2
19 https://doi.org/10.1056/nejmoa1003176
20 https://doi.org/10.1056/nejmoa1106920
21 https://doi.org/10.1056/nejmoa1107643
22 https://doi.org/10.1093/bioinformatics/btq167
23 https://doi.org/10.1093/bioinformatics/btq665
24 https://doi.org/10.1093/bioinformatics/btr652
25 https://doi.org/10.1093/bioinformatics/btu505
26 https://doi.org/10.1093/bioinformatics/btv689
27 https://doi.org/10.1093/nar/gkh340
28 https://doi.org/10.1093/nar/gkp919
29 https://doi.org/10.1093/nar/gkr1044
30 https://doi.org/10.1093/nar/gku1152
31 https://doi.org/10.1093/nar/gkw255
32 https://doi.org/10.1128/aem.00929-12
33 https://doi.org/10.1128/iai.00932-10
34 https://doi.org/10.1128/jb.00297-11
35 https://doi.org/10.1128/mbio.00565-13
36 https://doi.org/10.1371/journal.pone.0009490
37 https://doi.org/10.1371/journal.pone.0026624
38 https://doi.org/10.1371/journal.pone.0060120
39 https://doi.org/10.4161/gmic.2.1.14911
40 schema:datePublished 2017-12
41 schema:datePublishedReg 2017-12-01
42 schema:description BACKGROUND: The benefit of increasing genomic sequence data to the scientific community depends on easy-to-use, scalable bioinformatics support. CloVR-Comparative combines commonly used bioinformatics tools into an intuitive, automated, and cloud-enabled analysis pipeline for comparative microbial genomics. RESULTS: CloVR-Comparative runs on annotated complete or draft genome sequences that are uploaded by the user or selected via a taxonomic tree-based user interface and downloaded from NCBI. CloVR-Comparative runs reference-free multiple whole-genome alignments to determine unique, shared and core coding sequences (CDSs) and single nucleotide polymorphisms (SNPs). Output includes short summary reports and detailed text-based results files, graphical visualizations (phylogenetic trees, circular figures), and a database file linked to the Sybil comparative genome browser. Data up- and download, pipeline configuration and monitoring, and access to Sybil are managed through CloVR-Comparative web interface. CloVR-Comparative and Sybil are distributed as part of the CloVR virtual appliance, which runs on local computers or the Amazon EC2 cloud. Representative datasets (e.g. 40 draft and complete Escherichia coli genomes) are processed in <36 h on a local desktop or at a cost of <$20 on EC2. CONCLUSIONS: CloVR-Comparative allows anybody with Internet access to run comparative genomics projects, while eliminating the need for on-site computational resources and expertise.
43 schema:genre research_article
44 schema:inLanguage en
45 schema:isAccessibleForFree true
46 schema:isPartOf N26b46206d2984c42a919737d4c78dace
47 Ncc5cd8fc5ab446f3b47760d620ed50a1
48 sg:journal.1023790
49 schema:name CloVR-Comparative: automated, cloud-enabled comparative microbial genome sequence analysis pipeline
50 schema:pagination 332
51 schema:productId N29d25552df2041079b419e34955ab4dc
52 N7ce994fc73f942069de9dd4477f7f7f8
53 Naa265cfc985e46279ecdaf44f1c73bbe
54 Nb96340cd92524414badccad36cf0f55a
55 Nc53ba73d1bc9430580c8e07724c00ed8
56 schema:sameAs https://app.dimensions.ai/details/publication/pub.1084955821
57 https://doi.org/10.1186/s12864-017-3717-3
58 schema:sdDatePublished 2019-04-11T09:41
59 schema:sdLicense https://scigraph.springernature.com/explorer/license/
60 schema:sdPublisher Naecfc422dbb848728fad052b949c5eb2
61 schema:url https://link.springer.com/10.1186%2Fs12864-017-3717-3
62 sgo:license sg:explorer/license/
63 sgo:sdDataset articles
64 rdf:type schema:ScholarlyArticle
65 N06873936d2534eb3b9318c7097e51e67 schema:name Institute for Genome Sciences, Baltimore, MD, USA
66 rdf:type schema:Organization
67 N0b7508ecfe7140f3a4c5338dd283dca8 schema:name Institute for Genome Sciences, Baltimore, MD, USA
68 rdf:type schema:Organization
69 N0fd64de1f43340509de5407006c65545 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
70 schema:name Software
71 rdf:type schema:DefinedTerm
72 N12659c2283ec477fbe20013ee03f2739 schema:name Institute for Genome Sciences, Baltimore, MD, USA
73 rdf:type schema:Organization
74 N18f0b127b36f4288bb98f2d57b864b4f rdf:first sg:person.01123616342.98
75 rdf:rest N6ce9f2e30cb74e26b156af09cb27d42a
76 N26b46206d2984c42a919737d4c78dace schema:volumeNumber 18
77 rdf:type schema:PublicationVolume
78 N29d25552df2041079b419e34955ab4dc schema:name pubmed_id
79 schema:value 28449639
80 rdf:type schema:PropertyValue
81 N2a8477ffb7294ecbbc2641e9be768af2 rdf:first sg:person.01363437654.08
82 rdf:rest rdf:nil
83 N44c1f151ca1b43c9b114167dfb1a6a56 schema:name Institute for Genome Sciences, Baltimore, MD, USA
84 rdf:type schema:Organization
85 N4f699b312db144649f77948033ff377d rdf:first sg:person.01064750006.82
86 rdf:rest Ne1261c6ddd2f44448f248efbc34f3780
87 N5d80e6cbca674c2bae1322425aa0a51b rdf:first sg:person.01343322453.53
88 rdf:rest Ndbb2d2e8105a4de0bed0a10e51130e16
89 N5f480e5ab36c4702beb1c7f4d9627739 rdf:first sg:person.01117132167.66
90 rdf:rest Nb3e34ac571fb4965ad4a242d4381b921
91 N61ead7d9e68546fcbdaf609e33b264f1 schema:name Institute for Genome Sciences, Baltimore, MD, USA
92 rdf:type schema:Organization
93 N6553135f164f4d9b88e7e36af47a0717 schema:name Institute for Genome Sciences, Baltimore, MD, USA
94 rdf:type schema:Organization
95 N6b936c436d8949f6aaf34e1107a8e162 rdf:first sg:person.01333250544.05
96 rdf:rest Nade0ed749fbe426d8b6b1747faa2665e
97 N6ce9f2e30cb74e26b156af09cb27d42a rdf:first sg:person.01065620174.76
98 rdf:rest Na926dc19ce5640cab445b204de337153
99 N7b4b6e0ba94145fe94d4ac9c335250c3 schema:name Institute for Genome Sciences, Baltimore, MD, USA
100 rdf:type schema:Organization
101 N7ce994fc73f942069de9dd4477f7f7f8 schema:name doi
102 schema:value 10.1186/s12864-017-3717-3
103 rdf:type schema:PropertyValue
104 N9161e7dfb15149d5a95d8a8b4a790104 schema:name Institute for Genome Sciences, Baltimore, MD, USA
105 rdf:type schema:Organization
106 Na8f4402dbef64e299e0d054436a37ebf schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
107 schema:name Cloud Computing
108 rdf:type schema:DefinedTerm
109 Na926dc19ce5640cab445b204de337153 rdf:first sg:person.01021555477.04
110 rdf:rest N5d80e6cbca674c2bae1322425aa0a51b
111 Naa265cfc985e46279ecdaf44f1c73bbe schema:name dimensions_id
112 schema:value pub.1084955821
113 rdf:type schema:PropertyValue
114 Nade0ed749fbe426d8b6b1747faa2665e rdf:first sg:person.01267213104.21
115 rdf:rest N18f0b127b36f4288bb98f2d57b864b4f
116 Naecfc422dbb848728fad052b949c5eb2 schema:name Springer Nature - SN SciGraph project
117 rdf:type schema:Organization
118 Nb3e34ac571fb4965ad4a242d4381b921 rdf:first sg:person.010702355363.91
119 rdf:rest N4f699b312db144649f77948033ff377d
120 Nb96340cd92524414badccad36cf0f55a schema:name readcube_id
121 schema:value 40ce8bdfd43044c878c6a9806c3a97a5dca0d801aa5d7e1454188003d5da0e56
122 rdf:type schema:PropertyValue
123 Nc13bf5d243214c1d9d081cb67faa5121 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
124 schema:name Genome, Microbial
125 rdf:type schema:DefinedTerm
126 Nc2cccaa5cd5b4362b9cec53793bb2b16 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
127 schema:name Automation
128 rdf:type schema:DefinedTerm
129 Nc433b1b2893946c783f559db7cb7399b rdf:first sg:person.01042442240.45
130 rdf:rest N5f480e5ab36c4702beb1c7f4d9627739
131 Nc53ba73d1bc9430580c8e07724c00ed8 schema:name nlm_unique_id
132 schema:value 100965258
133 rdf:type schema:PropertyValue
134 Ncc5cd8fc5ab446f3b47760d620ed50a1 schema:issueNumber 1
135 rdf:type schema:PublicationIssue
136 Ndbb2d2e8105a4de0bed0a10e51130e16 rdf:first sg:person.01051370761.80
137 rdf:rest N2a8477ffb7294ecbbc2641e9be768af2
138 Ndea8e718919a45f5943429090814440c schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
139 schema:name Sequence Alignment
140 rdf:type schema:DefinedTerm
141 Ne1261c6ddd2f44448f248efbc34f3780 rdf:first sg:person.0773431027.21
142 rdf:rest N6b936c436d8949f6aaf34e1107a8e162
143 Neb257c8bf6dd4e4e9f4d922e9c9d4ce0 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
144 schema:name Sequence Analysis
145 rdf:type schema:DefinedTerm
146 Neb546a905ab042b288450af1a3487ba3 schema:name Institute for Genome Sciences, Baltimore, MD, USA
147 rdf:type schema:Organization
148 Nf6335b01b9db48e19e6d484067df989d schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
149 schema:name Genomics
150 rdf:type schema:DefinedTerm
151 anzsrc-for:08 schema:inDefinedTermSet anzsrc-for:
152 schema:name Information and Computing Sciences
153 rdf:type schema:DefinedTerm
154 anzsrc-for:0806 schema:inDefinedTermSet anzsrc-for:
155 schema:name Information Systems
156 rdf:type schema:DefinedTerm
157 sg:grant.2346893 http://pending.schema.org/fundedItem sg:pub.10.1186/s12864-017-3717-3
158 rdf:type schema:MonetaryGrant
159 sg:journal.1023790 schema:issn 1471-2164
160 schema:name BMC Genomics
161 rdf:type schema:Periodical
162 sg:person.01021555477.04 schema:affiliation https://www.grid.ac/institutes/grid.411024.2
163 schema:familyName White
164 schema:givenName Owen
165 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01021555477.04
166 rdf:type schema:Person
167 sg:person.01042442240.45 schema:affiliation N06873936d2534eb3b9318c7097e51e67
168 schema:familyName Agrawal
169 schema:givenName Sonia
170 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01042442240.45
171 rdf:type schema:Person
172 sg:person.01051370761.80 schema:affiliation N6553135f164f4d9b88e7e36af47a0717
173 schema:familyName Mahurkar
174 schema:givenName Anup
175 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01051370761.80
176 rdf:type schema:Person
177 sg:person.01064750006.82 schema:affiliation N0b7508ecfe7140f3a4c5338dd283dca8
178 schema:familyName Crabtree
179 schema:givenName Jonathan
180 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01064750006.82
181 rdf:type schema:Person
182 sg:person.01065620174.76 schema:affiliation https://www.grid.ac/institutes/grid.411024.2
183 schema:familyName Tettelin
184 schema:givenName Hervé
185 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01065620174.76
186 rdf:type schema:Person
187 sg:person.010702355363.91 schema:affiliation N44c1f151ca1b43c9b114167dfb1a6a56
188 schema:familyName Adkins
189 schema:givenName Ricky S.
190 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.010702355363.91
191 rdf:type schema:Person
192 sg:person.01117132167.66 schema:affiliation N7b4b6e0ba94145fe94d4ac9c335250c3
193 schema:familyName Arze
194 schema:givenName Cesar
195 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01117132167.66
196 rdf:type schema:Person
197 sg:person.01123616342.98 schema:affiliation https://www.grid.ac/institutes/grid.411024.2
198 schema:familyName Fraser
199 schema:givenName Claire M.
200 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01123616342.98
201 rdf:type schema:Person
202 sg:person.01267213104.21 schema:affiliation N12659c2283ec477fbe20013ee03f2739
203 schema:familyName Galens
204 schema:givenName Kevin
205 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01267213104.21
206 rdf:type schema:Person
207 sg:person.01333250544.05 schema:affiliation N9161e7dfb15149d5a95d8a8b4a790104
208 schema:familyName Vangala
209 schema:givenName Mahesh
210 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01333250544.05
211 rdf:type schema:Person
212 sg:person.01343322453.53 schema:affiliation Neb546a905ab042b288450af1a3487ba3
213 schema:familyName Angiuoli
214 schema:givenName Samuel V.
215 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01343322453.53
216 rdf:type schema:Person
217 sg:person.01363437654.08 schema:affiliation https://www.grid.ac/institutes/grid.9464.f
218 schema:familyName Fricke
219 schema:givenName W. Florian
220 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01363437654.08
221 rdf:type schema:Person
222 sg:person.0773431027.21 schema:affiliation N61ead7d9e68546fcbdaf609e33b264f1
223 schema:familyName Riley
224 schema:givenName David
225 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0773431027.21
226 rdf:type schema:Person
227 sg:pub.10.1007/s00203-011-0725-6 schema:sameAs https://app.dimensions.ai/details/publication/pub.1046599734
228 https://doi.org/10.1007/s00203-011-0725-6
229 rdf:type schema:CreativeWork
230 sg:pub.10.1038/npre.2011.5887.3 schema:sameAs https://app.dimensions.ai/details/publication/pub.1013539817
231 https://doi.org/10.1038/npre.2011.5887.3
232 rdf:type schema:CreativeWork
233 sg:pub.10.1186/1471-2105-12-272 schema:sameAs https://app.dimensions.ai/details/publication/pub.1033419151
234 https://doi.org/10.1186/1471-2105-12-272
235 rdf:type schema:CreativeWork
236 sg:pub.10.1186/1471-2105-12-356 schema:sameAs https://app.dimensions.ai/details/publication/pub.1026686709
237 https://doi.org/10.1186/1471-2105-12-356
238 rdf:type schema:CreativeWork
239 sg:pub.10.1186/1471-2105-6-2 schema:sameAs https://app.dimensions.ai/details/publication/pub.1001691322
240 https://doi.org/10.1186/1471-2105-6-2
241 rdf:type schema:CreativeWork
242 sg:pub.10.1186/gb-2004-5-2-r12 schema:sameAs https://app.dimensions.ai/details/publication/pub.1022585853
243 https://doi.org/10.1186/gb-2004-5-2-r12
244 rdf:type schema:CreativeWork
245 https://doi.org/10.1016/j.mib.2014.11.004 schema:sameAs https://app.dimensions.ai/details/publication/pub.1013381248
246 rdf:type schema:CreativeWork
247 https://doi.org/10.1016/s1473-3099(12)70268-2 schema:sameAs https://app.dimensions.ai/details/publication/pub.1035688197
248 rdf:type schema:CreativeWork
249 https://doi.org/10.1056/nejmoa1003176 schema:sameAs https://app.dimensions.ai/details/publication/pub.1043453056
250 rdf:type schema:CreativeWork
251 https://doi.org/10.1056/nejmoa1106920 schema:sameAs https://app.dimensions.ai/details/publication/pub.1002495373
252 rdf:type schema:CreativeWork
253 https://doi.org/10.1056/nejmoa1107643 schema:sameAs https://app.dimensions.ai/details/publication/pub.1013031508
254 rdf:type schema:CreativeWork
255 https://doi.org/10.1093/bioinformatics/btq167 schema:sameAs https://app.dimensions.ai/details/publication/pub.1015659639
256 rdf:type schema:CreativeWork
257 https://doi.org/10.1093/bioinformatics/btq665 schema:sameAs https://app.dimensions.ai/details/publication/pub.1002444689
258 rdf:type schema:CreativeWork
259 https://doi.org/10.1093/bioinformatics/btr652 schema:sameAs https://app.dimensions.ai/details/publication/pub.1048309275
260 rdf:type schema:CreativeWork
261 https://doi.org/10.1093/bioinformatics/btu505 schema:sameAs https://app.dimensions.ai/details/publication/pub.1036753823
262 rdf:type schema:CreativeWork
263 https://doi.org/10.1093/bioinformatics/btv689 schema:sameAs https://app.dimensions.ai/details/publication/pub.1042008257
264 rdf:type schema:CreativeWork
265 https://doi.org/10.1093/nar/gkh340 schema:sameAs https://app.dimensions.ai/details/publication/pub.1025846396
266 rdf:type schema:CreativeWork
267 https://doi.org/10.1093/nar/gkp919 schema:sameAs https://app.dimensions.ai/details/publication/pub.1050742720
268 rdf:type schema:CreativeWork
269 https://doi.org/10.1093/nar/gkr1044 schema:sameAs https://app.dimensions.ai/details/publication/pub.1028349189
270 rdf:type schema:CreativeWork
271 https://doi.org/10.1093/nar/gku1152 schema:sameAs https://app.dimensions.ai/details/publication/pub.1008767475
272 rdf:type schema:CreativeWork
273 https://doi.org/10.1093/nar/gkw255 schema:sameAs https://app.dimensions.ai/details/publication/pub.1017803216
274 rdf:type schema:CreativeWork
275 https://doi.org/10.1128/aem.00929-12 schema:sameAs https://app.dimensions.ai/details/publication/pub.1021965475
276 rdf:type schema:CreativeWork
277 https://doi.org/10.1128/iai.00932-10 schema:sameAs https://app.dimensions.ai/details/publication/pub.1010710799
278 rdf:type schema:CreativeWork
279 https://doi.org/10.1128/jb.00297-11 schema:sameAs https://app.dimensions.ai/details/publication/pub.1052942562
280 rdf:type schema:CreativeWork
281 https://doi.org/10.1128/mbio.00565-13 schema:sameAs https://app.dimensions.ai/details/publication/pub.1043224494
282 rdf:type schema:CreativeWork
283 https://doi.org/10.1371/journal.pone.0009490 schema:sameAs https://app.dimensions.ai/details/publication/pub.1000778834
284 rdf:type schema:CreativeWork
285 https://doi.org/10.1371/journal.pone.0026624 schema:sameAs https://app.dimensions.ai/details/publication/pub.1052415595
286 rdf:type schema:CreativeWork
287 https://doi.org/10.1371/journal.pone.0060120 schema:sameAs https://app.dimensions.ai/details/publication/pub.1053017354
288 rdf:type schema:CreativeWork
289 https://doi.org/10.4161/gmic.2.1.14911 schema:sameAs https://app.dimensions.ai/details/publication/pub.1072303866
290 rdf:type schema:CreativeWork
291 https://www.grid.ac/institutes/grid.411024.2 schema:alternateName University of Maryland, Baltimore
292 schema:name Department of Epidemiology, University of Maryland School of Medicine, Baltimore, MD, USA
293 Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
294 Institute for Genome Sciences, Baltimore, MD, USA
295 rdf:type schema:Organization
296 https://www.grid.ac/institutes/grid.9464.f schema:alternateName University of Hohenheim
297 schema:name Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
298 Department of Nutrigenomics, University of Hohenheim, Stuttgart, Germany
299 Institute for Genome Sciences, Baltimore, MD, USA
300 rdf:type schema:Organization
 




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


...