{"id":"https://openalex.org/W2143531254","doi":"https://doi.org/10.1093/bioinformatics/btt042","title":"essaMEM: finding maximal exact matches using enhanced sparse suffix arrays","display_name":"essaMEM: finding maximal exact matches using enhanced sparse suffix arrays","publication_year":2013,"publication_date":"2013-01-24","ids":{"openalex":"https://openalex.org/W2143531254","doi":"https://doi.org/10.1093/bioinformatics/btt042","mag":"2143531254","pmid":"https://pubmed.ncbi.nlm.nih.gov/23349213"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btt042","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt042","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/6/802/48898765/bioinformatics_29_6_802.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/29/6/802/48898765/bioinformatics_29_6_802.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5017206408","display_name":"Micha\u00ebl Vyverman","orcid":null},"institutions":[{"id":"https://openalex.org/I32597200","display_name":"Ghent University","ror":"https://ror.org/00cv9y106","country_code":"BE","type":"education","lineage":["https://openalex.org/I32597200"]}],"countries":["BE"],"is_corresponding":true,"raw_author_name":"Micha\u00ebl Vyverman","raw_affiliation_strings":["1 Department of Applied Mathematics and Computer Science and 2Department of Mathematical Modelling, Statistics and Bioinformatics, Ghent University, Ghent B-9000, Belgium"],"affiliations":[{"raw_affiliation_string":"1 Department of Applied Mathematics and Computer Science and 2Department of Mathematical Modelling, Statistics and Bioinformatics, Ghent University, Ghent B-9000, Belgium","institution_ids":["https://openalex.org/I32597200"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5012437460","display_name":"Bernard De Baets","orcid":"https://orcid.org/0000-0002-3876-620X"},"institutions":[{"id":"https://openalex.org/I32597200","display_name":"Ghent University","ror":"https://ror.org/00cv9y106","country_code":"BE","type":"education","lineage":["https://openalex.org/I32597200"]}],"countries":["BE"],"is_corresponding":false,"raw_author_name":"Bernard De Baets","raw_affiliation_strings":["1 Department of Applied Mathematics and Computer Science and 2Department of Mathematical Modelling, Statistics and Bioinformatics, Ghent University, Ghent B-9000, Belgium"],"affiliations":[{"raw_affiliation_string":"1 Department of Applied Mathematics and Computer Science and 2Department of Mathematical Modelling, Statistics and Bioinformatics, Ghent University, Ghent B-9000, Belgium","institution_ids":["https://openalex.org/I32597200"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080512219","display_name":"Veerle Fack","orcid":"https://orcid.org/0000-0002-0662-7176"},"institutions":[{"id":"https://openalex.org/I32597200","display_name":"Ghent University","ror":"https://ror.org/00cv9y106","country_code":"BE","type":"education","lineage":["https://openalex.org/I32597200"]}],"countries":["BE"],"is_corresponding":false,"raw_author_name":"Veerle Fack","raw_affiliation_strings":["1 Department of Applied Mathematics and Computer Science and 2Department of Mathematical Modelling, Statistics and Bioinformatics, Ghent University, Ghent B-9000, Belgium"],"affiliations":[{"raw_affiliation_string":"1 Department of Applied Mathematics and Computer Science and 2Department of Mathematical Modelling, Statistics and Bioinformatics, Ghent University, Ghent B-9000, Belgium","institution_ids":["https://openalex.org/I32597200"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5013637445","display_name":"Peter Dawyndt","orcid":"https://orcid.org/0000-0002-1623-9070"},"institutions":[{"id":"https://openalex.org/I32597200","display_name":"Ghent University","ror":"https://ror.org/00cv9y106","country_code":"BE","type":"education","lineage":["https://openalex.org/I32597200"]}],"countries":["BE"],"is_corresponding":false,"raw_author_name":"Peter Dawyndt","raw_affiliation_strings":["1 Department of Applied Mathematics and Computer Science and 2Department of Mathematical Modelling, Statistics and Bioinformatics, Ghent University, Ghent B-9000, Belgium"],"affiliations":[{"raw_affiliation_string":"1 Department of Applied Mathematics and Computer Science and 2Department of Mathematical Modelling, Statistics and Bioinformatics, Ghent University, Ghent B-9000, Belgium","institution_ids":["https://openalex.org/I32597200"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5017206408"],"corresponding_institution_ids":["https://openalex.org/I32597200"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":7.0066,"has_fulltext":true,"cited_by_count":54,"citation_normalized_percentile":{"value":0.96755383,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"29","issue":"6","first_page":"802","last_page":"804"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11269","display_name":"Algorithms and Data Compression","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T11269","display_name":"Algorithms and Data Compression","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9943000078201294,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T12326","display_name":"Network Packet Processing and Optimization","score":0.98089998960495,"subfield":{"id":"https://openalex.org/subfields/1708","display_name":"Hardware and Architecture"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/compressed-suffix-array","display_name":"Compressed suffix array","score":0.9232290983200073},{"id":"https://openalex.org/keywords/suffix","display_name":"Suffix","score":0.8957459926605225},{"id":"https://openalex.org/keywords/suffix-array","display_name":"Suffix array","score":0.878912627696991},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6478084325790405},{"id":"https://openalex.org/keywords/memory-footprint","display_name":"Memory footprint","score":0.5806518793106079},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.553674042224884},{"id":"https://openalex.org/keywords/sparse-array","display_name":"Sparse array","score":0.5412160754203796},{"id":"https://openalex.org/keywords/footprint","display_name":"Footprint","score":0.43504273891448975},{"id":"https://openalex.org/keywords/suffix-tree","display_name":"Suffix tree","score":0.41589608788490295},{"id":"https://openalex.org/keywords/data-structure","display_name":"Data structure","score":0.3601505756378174},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.34581345319747925},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.06983402371406555}],"concepts":[{"id":"https://openalex.org/C100903775","wikidata":"https://www.wikidata.org/wiki/Q5157028","display_name":"Compressed suffix array","level":4,"score":0.9232290983200073},{"id":"https://openalex.org/C2779804580","wikidata":"https://www.wikidata.org/wiki/Q102047","display_name":"Suffix","level":2,"score":0.8957459926605225},{"id":"https://openalex.org/C2779259728","wikidata":"https://www.wikidata.org/wiki/Q281472","display_name":"Suffix array","level":3,"score":0.878912627696991},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6478084325790405},{"id":"https://openalex.org/C74912251","wikidata":"https://www.wikidata.org/wiki/Q6815727","display_name":"Memory footprint","level":2,"score":0.5806518793106079},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.553674042224884},{"id":"https://openalex.org/C145177509","wikidata":"https://www.wikidata.org/wiki/Q1050404","display_name":"Sparse array","level":2,"score":0.5412160754203796},{"id":"https://openalex.org/C132943942","wikidata":"https://www.wikidata.org/wiki/Q2562511","display_name":"Footprint","level":2,"score":0.43504273891448975},{"id":"https://openalex.org/C2781166958","wikidata":"https://www.wikidata.org/wiki/Q1426863","display_name":"Suffix tree","level":3,"score":0.41589608788490295},{"id":"https://openalex.org/C162319229","wikidata":"https://www.wikidata.org/wiki/Q175263","display_name":"Data structure","level":2,"score":0.3601505756378174},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.34581345319747925},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.06983402371406555},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004330","descriptor_name":"Drosophila","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004330","descriptor_name":"Drosophila","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004330","descriptor_name":"Drosophila","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017421","descriptor_name":"Sequence Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017421","descriptor_name":"Sequence Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017421","descriptor_name":"Sequence Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btt042","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt042","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/6/802/48898765/bioinformatics_29_6_802.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:23349213","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23349213","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:archive.ugent.be:3195758","is_oa":false,"landing_page_url":"http://hdl.handle.net/1854/LU-3195758","pdf_url":null,"source":{"id":"https://openalex.org/S4306400478","display_name":"Ghent University Academic Bibliography (Ghent University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I32597200","host_organization_name":"Ghent University","host_organization_lineage":["https://openalex.org/I32597200"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"ISSN: 1367-4803","raw_type":"info:eu-repo/semantics/publishedVersion"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btt042","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt042","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/6/802/48898765/bioinformatics_29_6_802.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320319128","display_name":"Vlaams Supercomputer Centrum","ror":null},{"id":"https://openalex.org/F4320322603","display_name":"Universiteit Gent","ror":"https://ror.org/00cv9y106"},{"id":"https://openalex.org/F4320327336","display_name":"Vlaamse regering","ror":null}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2143531254.pdf","grobid_xml":"https://content.openalex.org/works/W2143531254.grobid-xml"},"referenced_works_count":7,"referenced_works":["https://openalex.org/W1487662321","https://openalex.org/W1573352354","https://openalex.org/W2088386938","https://openalex.org/W2093516854","https://openalex.org/W2107282968","https://openalex.org/W2134283755","https://openalex.org/W2171196697"],"related_works":["https://openalex.org/W2003608043","https://openalex.org/W2063841356","https://openalex.org/W2405149725","https://openalex.org/W2067974452","https://openalex.org/W2118703123","https://openalex.org/W4385595111","https://openalex.org/W153119118","https://openalex.org/W1527782099","https://openalex.org/W2014650117","https://openalex.org/W2950054934"],"abstract_inverted_index":{"We":[0],"have":[1],"developed":[2],"essaMEM,":[3],"a":[4,30],"tool":[5],"for":[6,40],"finding":[7,41],"maximal":[8,42],"exact":[9,43],"matches":[10,44],"that":[11,36],"can":[12],"be":[13],"used":[14],"in":[15],"genome":[16],"comparison":[17],"and":[18],"read":[19],"mapping.":[20],"essaMEM":[21],"enhances":[22],"an":[23],"existing":[24],"sparse":[25,31,57],"suffix":[26,58,67],"array":[27],"implementation":[28],"with":[29,62],"child":[32],"array.":[33],"Tests":[34],"indicate":[35],"the":[37,50,63],"enhanced":[38],"algorithm":[39],"is":[45],"much":[46],"faster,":[47],"while":[48],"maintaining":[49],"same":[51],"memory":[52],"footprint.":[53],"In":[54],"this":[55],"way,":[56],"arrays":[59],"remain":[60],"competitive":[61],"more":[64],"complex":[65],"compressed":[66],"arrays.":[68]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":5},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":9},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":8},{"year":2017,"cited_by_count":5},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":4},{"year":2014,"cited_by_count":7},{"year":2013,"cited_by_count":1}],"updated_date":"2026-04-03T22:45:19.894376","created_date":"2025-10-10T00:00:00"}