{"id":"https://openalex.org/W4225665859","doi":"https://doi.org/10.1186/s13015-021-00204-6","title":"An optimized FM-index library for nucleotide and amino acid search","display_name":"An optimized FM-index library for nucleotide and amino acid search","publication_year":2021,"publication_date":"2021-12-01","ids":{"openalex":"https://openalex.org/W4225665859","doi":"https://doi.org/10.1186/s13015-021-00204-6","pmid":"https://pubmed.ncbi.nlm.nih.gov/34972525"},"language":"en","primary_location":{"id":"doi:10.1186/s13015-021-00204-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13015-021-00204-6","pdf_url":"https://almob.biomedcentral.com/track/pdf/10.1186/s13015-021-00204-6","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/track/pdf/10.1186/s13015-021-00204-6","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5006457351","display_name":"Tim Anderson","orcid":null},"institutions":[{"id":"https://openalex.org/I6750721","display_name":"University of Montana","ror":"https://ror.org/0078xmk34","country_code":"US","type":"education","lineage":["https://openalex.org/I6750721"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Tim Anderson","raw_affiliation_strings":["Department of Computer Science, University of Montana, Missoula, MT, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Montana, Missoula, MT, USA","institution_ids":["https://openalex.org/I6750721"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5073174813","display_name":"Travis J. Wheeler","orcid":"https://orcid.org/0000-0003-2004-1785"},"institutions":[{"id":"https://openalex.org/I6750721","display_name":"University of Montana","ror":"https://ror.org/0078xmk34","country_code":"US","type":"education","lineage":["https://openalex.org/I6750721"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Travis J. Wheeler","raw_affiliation_strings":["Department of Computer Science, University of Montana, Missoula, MT, USA. travis.wheeler@umontana.edu","Department of Computer Science, University of Montana, Missoula, MT, USA"],"raw_orcid":"https://orcid.org/0000-0003-2004-1785","affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Montana, Missoula, MT, USA. travis.wheeler@umontana.edu","institution_ids":["https://openalex.org/I6750721"]},{"raw_affiliation_string":"Department of Computer Science, University of Montana, Missoula, MT, USA","institution_ids":["https://openalex.org/I6750721"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5073174813"],"corresponding_institution_ids":["https://openalex.org/I6750721"],"apc_list":{"value":1490,"currency":"GBP","value_usd":1827},"apc_paid":{"value":1490,"currency":"GBP","value_usd":1827},"fwci":0.681,"has_fulltext":true,"cited_by_count":10,"citation_normalized_percentile":{"value":0.76415526,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"16","issue":"1","first_page":"25","last_page":"25"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11269","display_name":"Algorithms and Data Compression","score":0.46230000257492065,"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":0.46230000257492065,"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/T12326","display_name":"Network Packet Processing and Optimization","score":0.20190000534057617,"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"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.1509999930858612,"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/index","display_name":"Index (typography)","score":0.6527606248855591},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6506047248840332},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.47636768221855164},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.4343389868736267},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3766401410102844},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.278999388217926},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.21682646870613098}],"concepts":[{"id":"https://openalex.org/C2777382242","wikidata":"https://www.wikidata.org/wiki/Q6017816","display_name":"Index (typography)","level":2,"score":0.6527606248855591},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6506047248840332},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.47636768221855164},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.4343389868736267},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3766401410102844},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.278999388217926},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.21682646870613098}],"mesh":[],"locations_count":7,"locations":[{"id":"doi:10.1186/s13015-021-00204-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13015-021-00204-6","pdf_url":"https://almob.biomedcentral.com/track/pdf/10.1186/s13015-021-00204-6","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:34972525","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34972525","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:doaj.org/article:cce5c4452d344971908b8d72a19c95e1","is_oa":true,"landing_page_url":"https://doaj.org/article/cce5c4452d344971908b8d72a19c95e1","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 16, Iss 1, Pp 1-13 (2021)","raw_type":"article"},{"id":"pmh:oai:osti.gov:1837844","is_oa":true,"landing_page_url":"https://www.osti.gov/biblio/1837844","pdf_url":null,"source":{"id":"https://openalex.org/S4306402487","display_name":"OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I139351228","host_organization_name":"Office of Scientific and Technical Information","host_organization_lineage":["https://openalex.org/I139351228"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null},{"id":"pmh:oai:osti.gov:1903221","is_oa":true,"landing_page_url":"https://www.osti.gov/biblio/1903221","pdf_url":null,"source":{"id":"https://openalex.org/S4306402487","display_name":"OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I139351228","host_organization_name":"Office of Scientific and Technical Information","host_organization_lineage":["https://openalex.org/I139351228"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null},{"id":"pmh:oai:osti.gov:2510975","is_oa":true,"landing_page_url":"https://www.osti.gov/servlets/purl/2510975","pdf_url":null,"source":{"id":"https://openalex.org/S4306402487","display_name":"OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I139351228","host_organization_name":"Office of Scientific and Technical Information","host_organization_lineage":["https://openalex.org/I139351228"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:8719400","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8719400","pdf_url":null,"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"}],"best_oa_location":{"id":"doi:10.1186/s13015-021-00204-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13015-021-00204-6","pdf_url":"https://almob.biomedcentral.com/track/pdf/10.1186/s13015-021-00204-6","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":[],"awards":[{"id":"https://openalex.org/G1055025889","display_name":null,"funder_award_id":"P20 GM103546","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G2454905030","display_name":null,"funder_award_id":"P20 GM103546","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G471773178","display_name":null,"funder_award_id":"DE-SC0021216","funder_id":"https://openalex.org/F4320337509","funder_display_name":"Biological and Environmental Research"},{"id":"https://openalex.org/G5111185494","display_name":null,"funder_award_id":"DE-SC0021216","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G540172779","display_name":null,"funder_award_id":"GM103546","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G8403458597","display_name":null,"funder_award_id":"DE-SC0021216","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G8932092815","display_name":null,"funder_award_id":"GM103546","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G954211639","display_name":null,"funder_award_id":"R01 HG002939","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"}],"funders":[{"id":"https://openalex.org/F4320306084","display_name":"U.S. Department of Energy","ror":"https://ror.org/01bj3aw27"},{"id":"https://openalex.org/F4320310589","display_name":"University of Montana","ror":"https://ror.org/0078xmk34"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337348","display_name":"National Human Genome Research Institute","ror":"https://ror.org/00baak391"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"},{"id":"https://openalex.org/F4320337509","display_name":"Biological and Environmental Research","ror":"https://ror.org/0114b2m14"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4225665859.pdf","grobid_xml":"https://content.openalex.org/works/W4225665859.grobid-xml"},"referenced_works_count":22,"referenced_works":["https://openalex.org/W17958277","https://openalex.org/W117230746","https://openalex.org/W1962019683","https://openalex.org/W2041445031","https://openalex.org/W2045204781","https://openalex.org/W2055043387","https://openalex.org/W2103441770","https://openalex.org/W2119279650","https://openalex.org/W2124985265","https://openalex.org/W2154139219","https://openalex.org/W2158874082","https://openalex.org/W2161048357","https://openalex.org/W2161488606","https://openalex.org/W2337747100","https://openalex.org/W2555913832","https://openalex.org/W2753396470","https://openalex.org/W2768599149","https://openalex.org/W2950954328","https://openalex.org/W2951160681","https://openalex.org/W2962735533","https://openalex.org/W3112376646","https://openalex.org/W6610688178"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W4391913857","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W4396696052"],"abstract_inverted_index":{"BACKGROUND:":[0],"Pattern":[1],"matching":[2],"is":[3,17,30,43,78,162,182,203,245],"a":[4,8,18,57,68,89,97,128,151,222,230],"key":[5],"step":[6],"in":[7,75,96,197],"variety":[9],"of":[10,32,35,40,56,106,122,153,229,237],"biological":[11],"sequence":[12],"analysis":[13],"pipelines.":[14],"The":[15,136,242],"FM-index":[16,42,61,72,94,108,148,218,239],"compressed":[19],"data":[20,95],"structure":[21],"for":[22,80,132,159,169,177,247],"pattern":[23],"matching,":[24],"with":[25,118,188,217],"search":[26],"run":[27],"time":[28],"that":[29,47,77,101],"independent":[31],"the":[33,36,41,54,107,123,194,238],"length":[34],"database":[37],"text.":[38],"Implementation":[39],"reasonably":[44],"complicated,":[45],"so":[46],"increased":[48],"adoption":[49],"will":[50],"be":[51],"aided":[52],"by":[53],"availability":[55],"fast":[58],"and":[59,83,115,127,142,172,214,233],"flexible":[60],"library.":[62],"RESULTS:":[63],"We":[64],"present":[65],"AvxWindowedFMindex":[66],"(AWFM-index),":[67],"lightweight,":[69],"open-source,":[70],"thread-parallel":[71],"library":[73,244],"written":[74],"C":[76],"optimized":[79,158],"indexing":[81],"nucleotide":[82,170],"amino":[84,178],"acid":[85,179],"sequences.":[86],"AWFM-index":[87,137,161,202],"introduces":[88],"new":[90],"approach":[91],"to":[92,205],"storing":[93,193],"strided":[98],"bit-vector":[99],"format":[100],"enables":[102],"extremely":[103],"efficient":[104],"computation":[105],"occurrence":[109],"function":[110],"via":[111],"AVX2":[112],"bitwise":[113],"instructions,":[114],"combines":[116],"this":[117],"optional":[119],"on-disk":[120,198],"storage":[121],"index's":[124],"suffix":[125,195],"array":[126,196],"cache-efficient":[129],"lookup":[130],"table":[131],"partial":[133],"k-mer":[134],"searches.":[135],"performs":[138],"exact":[139],"match":[140],"count":[141],"locate":[143,226],"queries":[144],"faster":[145,166,176,187],"than":[146,167],"SeqAn3's":[147],"implementation":[149],"across":[150],"range":[152],"comparable":[154],"memory":[155,190],"footprints.":[156],"When":[157],"speed,":[160],"[Formula:":[163,173,184],"see":[164,174,185],"text]2-4x":[165],"SeqAn3":[168],"search,":[171],"text]2-6x":[175],"search;":[180],"it":[181],"also":[183],"text]4x":[186],"similar":[189],"footprint":[191],"when":[192],"SSD":[199],"storage.":[200],"CONCLUSIONS:":[201],"easy":[204],"incorporate":[206],"into":[207],"bioinformatics":[208],"software,":[209],"offers":[210],"run-time":[211],"performance":[212],"parameterization,":[213],"provides":[215],"clients":[216],"functionality":[219],"at":[220,249],"both":[221],"high-level":[223],"(count":[224],"or":[225],"all":[227],"instances":[228],"query":[231],"string)":[232],"low-level":[234],"(step-wise":[235],"control":[236],"backward-search":[240],"process).":[241],"open-source":[243],"available":[246],"download":[248],"https://github.com/TravisWheelerLab/AvxWindowFmIndex.":[250]},"counts_by_year":[{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":4},{"year":2022,"cited_by_count":1}],"updated_date":"2026-07-02T09:51:11.867554","created_date":"2025-10-10T00:00:00"}
