Ontology type: schema:ScholarlyArticle Open Access: True
2009-03-04
AUTHORSBen Langmead, Cole Trapnell, Mihai Pop, Steven L Salzberg
ABSTRACTBowtie is an ultrafast, memory-efficient alignment program for aligning short DNA sequence reads to large genomes. For the human genome, Burrows-Wheeler indexing allows Bowtie to align more than 25 million reads per CPU hour with a memory footprint of approximately 1.3 gigabytes. Bowtie extends previous Burrows-Wheeler techniques with a novel quality-aware backtracking algorithm that permits mismatches. Multiple processor cores can be used simultaneously to achieve even greater alignment speeds. Bowtie is open source http://bowtie.cbcb.umd.edu. More... »
PAGESr25
http://scigraph.springernature.com/pub.10.1186/gb-2009-10-3-r25
DOIhttp://dx.doi.org/10.1186/gb-2009-10-3-r25
DIMENSIONShttps://app.dimensions.ai/details/publication/pub.1049583368
PUBMEDhttps://www.ncbi.nlm.nih.gov/pubmed/19261174
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": "Base Sequence",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Genome, Human",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Humans",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Sequence Alignment",
"type": "DefinedTerm"
}
],
"author": [
{
"affiliation": {
"alternateName": "Center for Bioinformatics and Computational Biology, Institute for Advanced Computer Studies, University of Maryland, 20742, College Park, MD, USA",
"id": "http://www.grid.ac/institutes/grid.164295.d",
"name": [
"Center for Bioinformatics and Computational Biology, Institute for Advanced Computer Studies, University of Maryland, 20742, College Park, MD, USA"
],
"type": "Organization"
},
"familyName": "Langmead",
"givenName": "Ben",
"id": "sg:person.011763134307.48",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.011763134307.48"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "Center for Bioinformatics and Computational Biology, Institute for Advanced Computer Studies, University of Maryland, 20742, College Park, MD, USA",
"id": "http://www.grid.ac/institutes/grid.164295.d",
"name": [
"Center for Bioinformatics and Computational Biology, Institute for Advanced Computer Studies, University of Maryland, 20742, College Park, MD, USA"
],
"type": "Organization"
},
"familyName": "Trapnell",
"givenName": "Cole",
"id": "sg:person.01247375013.30",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01247375013.30"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "Center for Bioinformatics and Computational Biology, Institute for Advanced Computer Studies, University of Maryland, 20742, College Park, MD, USA",
"id": "http://www.grid.ac/institutes/grid.164295.d",
"name": [
"Center for Bioinformatics and Computational Biology, Institute for Advanced Computer Studies, University of Maryland, 20742, College Park, MD, USA"
],
"type": "Organization"
},
"familyName": "Pop",
"givenName": "Mihai",
"id": "sg:person.01347372513.23",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01347372513.23"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "Center for Bioinformatics and Computational Biology, Institute for Advanced Computer Studies, University of Maryland, 20742, College Park, MD, USA",
"id": "http://www.grid.ac/institutes/grid.164295.d",
"name": [
"Center for Bioinformatics and Computational Biology, Institute for Advanced Computer Studies, University of Maryland, 20742, College Park, MD, USA"
],
"type": "Organization"
},
"familyName": "Salzberg",
"givenName": "Steven L",
"id": "sg:person.01223441713.02",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01223441713.02"
],
"type": "Person"
}
],
"citation": [
{
"id": "sg:pub.10.1038/nature07484",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1016969839",
"https://doi.org/10.1038/nature07484"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1186/1471-2105-9-11",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1049945398",
"https://doi.org/10.1186/1471-2105-9-11"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/ng.195",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1031106868",
"https://doi.org/10.1038/ng.195"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/ng.128",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1047246435",
"https://doi.org/10.1038/ng.128"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/nbt1414",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1030992136",
"https://doi.org/10.1038/nbt1414"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1186/1471-2105-9-128",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1029892891",
"https://doi.org/10.1186/1471-2105-9-128"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/nature07517",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1052925719",
"https://doi.org/10.1038/nature07517"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/nature07485",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1034796960",
"https://doi.org/10.1038/nature07485"
],
"type": "CreativeWork"
}
],
"datePublished": "2009-03-04",
"datePublishedReg": "2009-03-04",
"description": "Bowtie is an ultrafast, memory-efficient alignment program for aligning short DNA sequence reads to large genomes. For the human genome, Burrows-Wheeler indexing allows Bowtie to align more than 25 million reads per CPU hour with a memory footprint of approximately 1.3 gigabytes. Bowtie extends previous Burrows-Wheeler techniques with a novel quality-aware backtracking algorithm that permits mismatches. Multiple processor cores can be used simultaneously to achieve even greater alignment speeds. Bowtie is open source http://bowtie.cbcb.umd.edu.",
"genre": "article",
"id": "sg:pub.10.1186/gb-2009-10-3-r25",
"inLanguage": "en",
"isAccessibleForFree": true,
"isFundedItemOf": [
{
"id": "sg:grant.2529352",
"type": "MonetaryGrant"
},
{
"id": "sg:grant.2519905",
"type": "MonetaryGrant"
},
{
"id": "sg:grant.2545461",
"type": "MonetaryGrant"
}
],
"isPartOf": [
{
"id": "sg:journal.1023439",
"issn": [
"1474-760X",
"1465-6906"
],
"name": "Genome Biology",
"publisher": "Springer Nature",
"type": "Periodical"
},
{
"issueNumber": "3",
"type": "PublicationIssue"
},
{
"type": "PublicationVolume",
"volumeNumber": "10"
}
],
"keywords": [
"multiple processor cores",
"memory footprint",
"open source",
"processor cores",
"backtracking algorithm",
"alignment speed",
"CPU hours",
"alignment programs",
"gigabytes",
"indexing",
"algorithm",
"short DNA sequences",
"bowtie",
"speed",
"footprint",
"technique",
"alignment",
"reads",
"sequence",
"large genomes",
"program",
"human genome",
"core",
"mismatch",
"DNA sequences",
"source",
"genome",
"hours"
],
"name": "Ultrafast and memory-efficient alignment of short DNA sequences to the human genome",
"pagination": "r25",
"productId": [
{
"name": "dimensions_id",
"type": "PropertyValue",
"value": [
"pub.1049583368"
]
},
{
"name": "doi",
"type": "PropertyValue",
"value": [
"10.1186/gb-2009-10-3-r25"
]
},
{
"name": "pubmed_id",
"type": "PropertyValue",
"value": [
"19261174"
]
}
],
"sameAs": [
"https://doi.org/10.1186/gb-2009-10-3-r25",
"https://app.dimensions.ai/details/publication/pub.1049583368"
],
"sdDataset": "articles",
"sdDatePublished": "2022-05-10T09:59",
"sdLicense": "https://scigraph.springernature.com/explorer/license/",
"sdPublisher": {
"name": "Springer Nature - SN SciGraph project",
"type": "Organization"
},
"sdSource": "s3://com-springernature-scigraph/baseset/20220509/entities/gbq_results/article/article_494.jsonl",
"type": "ScholarlyArticle",
"url": "https://doi.org/10.1186/gb-2009-10-3-r25"
}
]Download the RDF metadata as:Â json-ld nt turtle xml License info
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/gb-2009-10-3-r25'
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/gb-2009-10-3-r25'
Turtle is a human-readable linked data format.
curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1186/gb-2009-10-3-r25'
RDF/XML is a standard XML format for linked data.
curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1186/gb-2009-10-3-r25'
This table displays all metadata directly associated to this object as RDF triples.
169 TRIPLES
22 PREDICATES
67 URIs
51 LITERALS
12 BLANK NODES