{"id":"https://openalex.org/W4394688386","doi":"https://doi.org/10.1186/s13015-024-00260-8","title":"Pfp-fm: an accelerated FM-index","display_name":"Pfp-fm: an accelerated FM-index","publication_year":2024,"publication_date":"2024-04-10","ids":{"openalex":"https://openalex.org/W4394688386","doi":"https://doi.org/10.1186/s13015-024-00260-8","pmid":"https://pubmed.ncbi.nlm.nih.gov/38600518"},"language":"en","primary_location":{"id":"doi:10.1186/s13015-024-00260-8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13015-024-00260-8","pdf_url":"https://almob.biomedcentral.com/counter/pdf/10.1186/s13015-024-00260-8","source":{"id":"https://openalex.org/S205663195","display_name":"Algorithms for Molecular Biology","issn_l":"1748-7188","issn":["1748-7188"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Algorithms for Molecular Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://almob.biomedcentral.com/counter/pdf/10.1186/s13015-024-00260-8","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5040283964","display_name":"Aaron Hong","orcid":"https://orcid.org/0000-0002-1361-7216"},"institutions":[{"id":"https://openalex.org/I33213144","display_name":"University of Florida","ror":"https://ror.org/02y3ad647","country_code":"US","type":"education","lineage":["https://openalex.org/I33213144"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Aaron Hong","raw_affiliation_strings":["Department of Computer and Information Science and Engineering, University of Florida, Gainesville, Florida, 32611, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer and Information Science and Engineering, University of Florida, Gainesville, Florida, 32611, USA","institution_ids":["https://openalex.org/I33213144"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5020831803","display_name":"Marco Ant\u00f4nio Oliva","orcid":"https://orcid.org/0000-0003-0525-3114"},"institutions":[{"id":"https://openalex.org/I33213144","display_name":"University of Florida","ror":"https://ror.org/02y3ad647","country_code":"US","type":"education","lineage":["https://openalex.org/I33213144"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Marco Oliva","raw_affiliation_strings":["Department of Computer and Information Science and Engineering, University of Florida, Gainesville, Florida, 32611, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer and Information Science and Engineering, University of Florida, Gainesville, Florida, 32611, USA","institution_ids":["https://openalex.org/I33213144"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071551582","display_name":"Dominik K\u00f6ppl","orcid":"https://orcid.org/0000-0002-8721-4444"},"institutions":[{"id":"https://openalex.org/I125602781","display_name":"Tokyo Medical and Dental University","ror":"https://ror.org/051k3eh31","country_code":"JP","type":"education","lineage":["https://openalex.org/I125602781"]},{"id":"https://openalex.org/I66906201","display_name":"University of Yamanashi","ror":"https://ror.org/059x21724","country_code":"JP","type":"education","lineage":["https://openalex.org/I66906201"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Dominik K\u00f6ppl","raw_affiliation_strings":["Faculty of Engineering, University of Yamanashi, K\u014dfu, 400-8510, Japan","M &D Data Science Center, Tokyo Medical and Dental University, Tokyo, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Engineering, University of Yamanashi, K\u014dfu, 400-8510, Japan","institution_ids":["https://openalex.org/I66906201"]},{"raw_affiliation_string":"M &D Data Science Center, Tokyo Medical and Dental University, Tokyo, Japan","institution_ids":["https://openalex.org/I125602781"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5011046118","display_name":"Hideo Bannai","orcid":"https://orcid.org/0000-0002-6856-5185"},"institutions":[{"id":"https://openalex.org/I125602781","display_name":"Tokyo Medical and Dental University","ror":"https://ror.org/051k3eh31","country_code":"JP","type":"education","lineage":["https://openalex.org/I125602781"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Hideo Bannai","raw_affiliation_strings":["M &D Data Science Center, Tokyo Medical and Dental University, Tokyo, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"M &D Data Science Center, Tokyo Medical and Dental University, Tokyo, Japan","institution_ids":["https://openalex.org/I125602781"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021635660","display_name":"Christina Boucher","orcid":"https://orcid.org/0000-0001-9509-9725"},"institutions":[{"id":"https://openalex.org/I33213144","display_name":"University of Florida","ror":"https://ror.org/02y3ad647","country_code":"US","type":"education","lineage":["https://openalex.org/I33213144"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Christina Boucher","raw_affiliation_strings":["Department of Computer and Information Science and Engineering, University of Florida, Gainesville, Florida, 32611, USA. christinaboucher@ufl.edu","Department of Computer and Information Science and Engineering, University of Florida, Gainesville, Florida, 32611, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer and Information Science and Engineering, University of Florida, Gainesville, Florida, 32611, USA. christinaboucher@ufl.edu","institution_ids":["https://openalex.org/I33213144"]},{"raw_affiliation_string":"Department of Computer and Information Science and Engineering, University of Florida, Gainesville, Florida, 32611, USA","institution_ids":["https://openalex.org/I33213144"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5013172801","display_name":"Travis Gagie","orcid":"https://orcid.org/0000-0003-3689-327X"},"institutions":[{"id":"https://openalex.org/I129902397","display_name":"Dalhousie University","ror":"https://ror.org/01e6qks80","country_code":"CA","type":"education","lineage":["https://openalex.org/I129902397"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Travis Gagie","raw_affiliation_strings":["Faculty of Computer Science, Dalhousie University, Halifax, Nova Scotia, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Computer Science, Dalhousie University, Halifax, Nova Scotia, Canada","institution_ids":["https://openalex.org/I129902397"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5021635660"],"corresponding_institution_ids":["https://openalex.org/I33213144"],"apc_list":{"value":2290,"currency":"USD","value_usd":2290},"apc_paid":{"value":2290,"currency":"USD","value_usd":2290},"fwci":1.4581,"has_fulltext":true,"cited_by_count":6,"citation_normalized_percentile":{"value":0.83551175,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":97},"biblio":{"volume":"19","issue":"1","first_page":"15","last_page":"15"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11269","display_name":"Algorithms and Data Compression","score":0.9998000264167786,"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":0.9998000264167786,"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":0.9991000294685364,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9894999861717224,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8157691359519958},{"id":"https://openalex.org/keywords/parsing","display_name":"Parsing","score":0.7995167970657349},{"id":"https://openalex.org/keywords/suffix","display_name":"Suffix","score":0.7715829014778137},{"id":"https://openalex.org/keywords/word","display_name":"Word (group theory)","score":0.6130804419517517},{"id":"https://openalex.org/keywords/sorting","display_name":"Sorting","score":0.580962061882019},{"id":"https://openalex.org/keywords/search-engine-indexing","display_name":"Search engine indexing","score":0.5295720100402832},{"id":"https://openalex.org/keywords/prefix","display_name":"Prefix","score":0.5063835382461548},{"id":"https://openalex.org/keywords/character","display_name":"Character (mathematics)","score":0.48302826285362244},{"id":"https://openalex.org/keywords/suffix-array","display_name":"Suffix array","score":0.4753546416759491},{"id":"https://openalex.org/keywords/index","display_name":"Index (typography)","score":0.43912553787231445},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.41929590702056885},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.37923717498779297},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.3379119634628296},{"id":"https://openalex.org/keywords/data-structure","display_name":"Data structure","score":0.2104400396347046},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.10688695311546326},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.10525515675544739}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8157691359519958},{"id":"https://openalex.org/C186644900","wikidata":"https://www.wikidata.org/wiki/Q194152","display_name":"Parsing","level":2,"score":0.7995167970657349},{"id":"https://openalex.org/C2779804580","wikidata":"https://www.wikidata.org/wiki/Q102047","display_name":"Suffix","level":2,"score":0.7715829014778137},{"id":"https://openalex.org/C90805587","wikidata":"https://www.wikidata.org/wiki/Q10944557","display_name":"Word (group theory)","level":2,"score":0.6130804419517517},{"id":"https://openalex.org/C111696304","wikidata":"https://www.wikidata.org/wiki/Q2303697","display_name":"Sorting","level":2,"score":0.580962061882019},{"id":"https://openalex.org/C75165309","wikidata":"https://www.wikidata.org/wiki/Q2258979","display_name":"Search engine indexing","level":2,"score":0.5295720100402832},{"id":"https://openalex.org/C141603448","wikidata":"https://www.wikidata.org/wiki/Q134830","display_name":"Prefix","level":2,"score":0.5063835382461548},{"id":"https://openalex.org/C2780861071","wikidata":"https://www.wikidata.org/wiki/Q1062934","display_name":"Character (mathematics)","level":2,"score":0.48302826285362244},{"id":"https://openalex.org/C2779259728","wikidata":"https://www.wikidata.org/wiki/Q281472","display_name":"Suffix array","level":3,"score":0.4753546416759491},{"id":"https://openalex.org/C2777382242","wikidata":"https://www.wikidata.org/wiki/Q6017816","display_name":"Index (typography)","level":2,"score":0.43912553787231445},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.41929590702056885},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.37923717498779297},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.3379119634628296},{"id":"https://openalex.org/C162319229","wikidata":"https://www.wikidata.org/wiki/Q175263","display_name":"Data structure","level":2,"score":0.2104400396347046},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.10688695311546326},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.10525515675544739},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1186/s13015-024-00260-8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13015-024-00260-8","pdf_url":"https://almob.biomedcentral.com/counter/pdf/10.1186/s13015-024-00260-8","source":{"id":"https://openalex.org/S205663195","display_name":"Algorithms for Molecular Biology","issn_l":"1748-7188","issn":["1748-7188"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Algorithms for Molecular Biology","raw_type":"journal-article"},{"id":"pmid:38600518","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38600518","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":"Algorithms for molecular biology : AMB","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:11005213","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11005213","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11005213/pdf/13015_2024_Article_260.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Algorithms Mol Biol","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:5d545f4b58b649eaad33789914714512","is_oa":true,"landing_page_url":"https://doaj.org/article/5d545f4b58b649eaad33789914714512","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Algorithms for Molecular Biology, Vol 19, Iss 1, Pp 1-14 (2024)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/s13015-024-00260-8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13015-024-00260-8","pdf_url":"https://almob.biomedcentral.com/counter/pdf/10.1186/s13015-024-00260-8","source":{"id":"https://openalex.org/S205663195","display_name":"Algorithms for Molecular Biology","issn_l":"1748-7188","issn":["1748-7188"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Algorithms for Molecular Biology","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.46000000834465027,"id":"https://metadata.un.org/sdg/4","display_name":"Quality Education"}],"awards":[{"id":"https://openalex.org/G1646130523","display_name":null,"funder_award_id":"DBI-2029552","funder_id":"https://openalex.org/F4320332167","funder_display_name":"Directorate for Biological Sciences"},{"id":"https://openalex.org/G2099009234","display_name":null,"funder_award_id":"R01AI14180","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"},{"id":"https://openalex.org/G2177795867","display_name":null,"funder_award_id":"JP23H04378","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G2241781793","display_name":null,"funder_award_id":"R01HG011392","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G2341366841","display_name":null,"funder_award_id":"DBI-2029552","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G2344728784","display_name":null,"funder_award_id":"RGPIN071852020","funder_id":"https://openalex.org/F4320334593","funder_display_name":"Natural Sciences and Engineering Research Council of Canada"},{"id":"https://openalex.org/G2673869144","display_name":"SCH: INT: Enabling real time surveillance of antimicrobial resistance","funder_award_id":"2013998","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G270470657","display_name":"IIBR Informatics: An Efficient Pangenomics Graph Aligner","funder_award_id":"2029552","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G3396921939","display_name":null,"funder_award_id":"2013998","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G4091776703","display_name":"Combinatorics of string lexicographic orders and their applications","funder_award_id":"20H04141","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G4132520530","display_name":null,"funder_award_id":"R01AI14180","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"},{"id":"https://openalex.org/G5050383059","display_name":null,"funder_award_id":"R01HG011392","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"},{"id":"https://openalex.org/G5063834206","display_name":null,"funder_award_id":"JP20H04141","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G6021068785","display_name":null,"funder_award_id":"JP22H03551","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G7077011381","display_name":null,"funder_award_id":"2029552","funder_id":"https://openalex.org/F4320332167","funder_display_name":"Directorate for Biological Sciences"},{"id":"https://openalex.org/G7579068829","display_name":null,"funder_award_id":"23H04378","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G8223816068","display_name":null,"funder_award_id":"INT-2013998","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G8512566826","display_name":null,"funder_award_id":"RGPIN-07185-2020","funder_id":"https://openalex.org/F4320334593","funder_display_name":"Natural Sciences and Engineering Research Council of Canada"},{"id":"https://openalex.org/G8675867022","display_name":null,"funder_award_id":"JP21K17701","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G8763578522","display_name":null,"funder_award_id":"R01 HG011392","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"},{"id":"https://openalex.org/G8833507762","display_name":null,"funder_award_id":"R01AI14180","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320332167","display_name":"Directorate for Biological Sciences","ror":"https://ror.org/001xhss06"},{"id":"https://openalex.org/F4320334593","display_name":"Natural Sciences and Engineering Research Council of Canada","ror":"https://ror.org/01h531d29"},{"id":"https://openalex.org/F4320334764","display_name":"Japan Society for the Promotion of Science","ror":"https://ror.org/00hhkn466"},{"id":"https://openalex.org/F4320337348","display_name":"National Human Genome Research Institute","ror":"https://ror.org/00baak391"},{"id":"https://openalex.org/F4320337355","display_name":"National Institute of Allergy and Infectious Diseases","ror":"https://ror.org/043z4tv69"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4394688386.pdf"},"referenced_works_count":25,"referenced_works":["https://openalex.org/W1485941238","https://openalex.org/W1524202346","https://openalex.org/W1554611468","https://openalex.org/W1826264422","https://openalex.org/W2031234611","https://openalex.org/W2124985265","https://openalex.org/W2150749717","https://openalex.org/W2158874082","https://openalex.org/W2159647614","https://openalex.org/W2170551349","https://openalex.org/W2811012751","https://openalex.org/W2889833303","https://openalex.org/W2952597168","https://openalex.org/W2963653132","https://openalex.org/W2963972957","https://openalex.org/W2999295646","https://openalex.org/W3011828211","https://openalex.org/W3122109253","https://openalex.org/W3203180644","https://openalex.org/W3203691570","https://openalex.org/W4210644165","https://openalex.org/W4251086285","https://openalex.org/W4315784849","https://openalex.org/W4386240935","https://openalex.org/W4394666350"],"related_works":["https://openalex.org/W2022951409","https://openalex.org/W4385652842","https://openalex.org/W3196825089","https://openalex.org/W4368367671","https://openalex.org/W2413189204","https://openalex.org/W3012663989","https://openalex.org/W4318200119","https://openalex.org/W2773803767","https://openalex.org/W2738126475","https://openalex.org/W2063556310"],"abstract_inverted_index":{"Abstract":[0],"FM-indexes":[1,86,93],"are":[2,96],"crucial":[3],"data":[4,75],"structures":[5],"in":[6,22,31,193],"DNA":[7,50],"alignment,":[8],"but":[9],"searching":[10],"with":[11,189],"them":[12],"usually":[13],"takes":[14,112],"at":[15,212],"least":[16],"one":[17],"random":[18,39],"access":[19],"per":[20],"character":[21],"the":[23,83,118,122,181,194],"query":[24],"pattern.":[25],"Ferragina":[26],"and":[27,44,80,144,150,161,171],"Fischer":[28],"[1]":[29],"observed":[30],"2007":[32],"that":[33,82,108,114],"word-based":[34,64,85],"indexes":[35],"often":[36],"use":[37],"fewer":[38],"accesses":[40],"than":[41,91,154],"character-based":[42],"indexes,":[43],"thus":[45],"support":[46,87],"faster":[47,88,153,164],"searches.":[48],"Since":[49],"lacks":[51],"natural":[52],"word-boundaries,":[53],"however,":[54],"it":[55,60,146,176],"is":[56,147,162,210],"necessary":[57],"to":[58,159,168],"parse":[59],"somehow":[61],"before":[62],"applying":[63],"FM-indexing.":[65],"In":[66,103],"2022,":[67],"Deng":[68],"et":[69],"al.":[70],"[2]":[71],"proposed":[72],"parsing":[73],"genomic":[74],"by":[76],"induced":[77,125],"suffix":[78,126],"sorting,":[79,127],"showed":[81],"resulting":[84],"counting":[89],"queries":[90,158,166],"standard":[92],"when":[94],"patterns":[95,133],"a":[97,129,136,190],"few":[98,137],"thousand":[99],"characters":[100],"or":[101],"longer.":[102],"this":[104],"paper":[105],"we":[106],"show":[107],"using":[109],"prefix-free":[110],"parsing\u2014which":[111],"parameters":[113],"let":[115],"us":[116],"tune":[117],"average":[119],"length":[120],"of":[121,124,134,183],"phrases\u2014instead":[123],"gives":[128],"significant":[130],"speedup":[131],"for":[132,199],"only":[135],"hundred":[138],"characters.":[139],"We":[140],"implement":[141],"our":[142,178],"method":[143,179],"demonstrate":[145],"between":[148],"3":[149],"18":[151],"times":[152],"competing":[155],"methods":[156,188],"on":[157,165],"GRCh38,":[160],"consistently":[163],"made":[167],"25,000,":[169],"50,000":[170],"100,000":[172],"SARS-CoV-2":[173],"genomes.":[174],"Hence,":[175],"seems":[177],"accelerates":[180],"performance":[182],"count":[184],"over":[185],"all":[186],"state-of-the-art":[187],"moderate":[191],"increase":[192],"memory.":[195],"The":[196],"source":[197],"code":[198],"$$\\texttt":[200],"{PFP-FM}$$":[201],"<mml:math":[202],"xmlns:mml=\"http://www.w3.org/1998/Math/MathML\">":[203],"<mml:mrow>":[204],"<mml:mi>PFP</mml:mi>":[205],"<mml:mo>-</mml:mo>":[206],"<mml:mi>FM</mml:mi>":[207],"</mml:mrow>":[208],"</mml:math>":[209],"available":[211],"https://github.com/AaronHong1024/afm":[213],".":[214]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":2}],"updated_date":"2026-07-23T08:03:31.855105","created_date":"2025-10-10T00:00:00"}