{"id":"https://openalex.org/W2011289056","doi":"https://doi.org/10.1371/journal.pcbi.1000392","title":"Fast Statistical Alignment","display_name":"Fast Statistical Alignment","publication_year":2009,"publication_date":"2009-05-28","ids":{"openalex":"https://openalex.org/W2011289056","doi":"https://doi.org/10.1371/journal.pcbi.1000392","mag":"2011289056","pmid":"https://pubmed.ncbi.nlm.nih.gov/19478997"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1000392","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1000392","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1000392&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1000392&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5032741707","display_name":"Robert K. Bradley","orcid":"https://orcid.org/0000-0002-8046-1063"},"institutions":[{"id":"https://openalex.org/I95457486","display_name":"University of California, Berkeley","ror":"https://ror.org/01an7q238","country_code":"US","type":"education","lineage":["https://openalex.org/I95457486"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Robert K. Bradley","raw_affiliation_strings":["Department of Mathematics, University of California Berkeley, Berkeley, California, United States of America. rbradley@berkeley.edu","Department of Molecular & Cellular Biology, University of California Berkeley, Berkeley, California, United States of America","Department of Mathematics, University of California Berkeley, Berkeley, California, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Mathematics, University of California Berkeley, Berkeley, California, United States of America. rbradley@berkeley.edu","institution_ids":["https://openalex.org/I95457486"]},{"raw_affiliation_string":"Department of Molecular & Cellular Biology, University of California Berkeley, Berkeley, California, United States of America","institution_ids":["https://openalex.org/I95457486"]},{"raw_affiliation_string":"Department of Mathematics, University of California Berkeley, Berkeley, California, United States of America","institution_ids":["https://openalex.org/I95457486"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042650280","display_name":"Adam Roberts","orcid":"https://orcid.org/0000-0003-3539-804X"},"institutions":[{"id":"https://openalex.org/I95457486","display_name":"University of California, Berkeley","ror":"https://ror.org/01an7q238","country_code":"US","type":"education","lineage":["https://openalex.org/I95457486"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Adam Roberts","raw_affiliation_strings":["Department of Electrical Engineering & Computer Science, University of California Berkeley, Berkeley, California, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Electrical Engineering & Computer Science, University of California Berkeley, Berkeley, California, United States of America","institution_ids":["https://openalex.org/I95457486"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5068272466","display_name":"Michael Smoot","orcid":"https://orcid.org/0000-0002-0584-6537"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Michael Smoot","raw_affiliation_strings":["Department of Bioengineering, University of California San Diego, San Diego, California, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of California San Diego, San Diego, California, United States of America","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5014148410","display_name":"Sudeep Juvekar","orcid":null},"institutions":[{"id":"https://openalex.org/I95457486","display_name":"University of California, Berkeley","ror":"https://ror.org/01an7q238","country_code":"US","type":"education","lineage":["https://openalex.org/I95457486"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sudeep Juvekar","raw_affiliation_strings":["Department of Electrical Engineering & Computer Science, University of California Berkeley, Berkeley, California, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Electrical Engineering & Computer Science, University of California Berkeley, Berkeley, California, United States of America","institution_ids":["https://openalex.org/I95457486"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024989829","display_name":"Jaeyoung Do","orcid":"https://orcid.org/0000-0003-1275-1621"},"institutions":[{"id":"https://openalex.org/I135310074","display_name":"University of Wisconsin\u2013Madison","ror":"https://ror.org/01y2jtd41","country_code":"US","type":"education","lineage":["https://openalex.org/I135310074"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jaeyoung Do","raw_affiliation_strings":["Department of Computer Sciences, University of Wisconsin, Madison, Wisconsin, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Computer Sciences, University of Wisconsin, Madison, Wisconsin, United States of America","institution_ids":["https://openalex.org/I135310074"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032698492","display_name":"Colin N. Dewey","orcid":"https://orcid.org/0000-0003-1498-9254"},"institutions":[{"id":"https://openalex.org/I135310074","display_name":"University of Wisconsin\u2013Madison","ror":"https://ror.org/01y2jtd41","country_code":"US","type":"education","lineage":["https://openalex.org/I135310074"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Colin Dewey","raw_affiliation_strings":["Department of Biostatistics & Medical Informatics, University of Wisconsin, Madison, Wisconsin, United States of America","Department of Computer Sciences, University of Wisconsin, Madison, Wisconsin, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Biostatistics & Medical Informatics, University of Wisconsin, Madison, Wisconsin, United States of America","institution_ids":["https://openalex.org/I135310074"]},{"raw_affiliation_string":"Department of Computer Sciences, University of Wisconsin, Madison, Wisconsin, United States of America","institution_ids":["https://openalex.org/I135310074"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054625887","display_name":"Ian Holmes","orcid":"https://orcid.org/0000-0001-7639-5369"},"institutions":[{"id":"https://openalex.org/I95457486","display_name":"University of California, Berkeley","ror":"https://ror.org/01an7q238","country_code":"US","type":"education","lineage":["https://openalex.org/I95457486"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ian Holmes","raw_affiliation_strings":["Department of Bioengineering, University of California Berkeley, Berkeley, California, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of California Berkeley, Berkeley, California, United States of America","institution_ids":["https://openalex.org/I95457486"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5020008219","display_name":"Lior Pachter","orcid":"https://orcid.org/0000-0002-9164-6231"},"institutions":[{"id":"https://openalex.org/I95457486","display_name":"University of California, Berkeley","ror":"https://ror.org/01an7q238","country_code":"US","type":"education","lineage":["https://openalex.org/I95457486"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Lior Pachter","raw_affiliation_strings":["Department of Mathematics, University of California Berkeley, Berkeley, California, United States of America","Department of Molecular & Cellular Biology, University of California Berkeley, Berkeley, California, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Mathematics, University of California Berkeley, Berkeley, California, United States of America","institution_ids":["https://openalex.org/I95457486"]},{"raw_affiliation_string":"Department of Molecular & Cellular Biology, University of California Berkeley, Berkeley, California, United States of America","institution_ids":["https://openalex.org/I95457486"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":8,"corresponding_author_ids":["https://openalex.org/A5032741707"],"corresponding_institution_ids":["https://openalex.org/I95457486"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":14.1548,"has_fulltext":true,"cited_by_count":371,"citation_normalized_percentile":{"value":0.99364305,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":100},"biblio":{"volume":"5","issue":"5","first_page":"e1000392","last_page":"e1000392"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9998000264167786,"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"}},"topics":[{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9998000264167786,"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/T11269","display_name":"Algorithms and Data Compression","score":0.9937999844551086,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9848999977111816,"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":0.7576150894165039},{"id":"https://openalex.org/keywords/multiple-sequence-alignment","display_name":"Multiple sequence alignment","score":0.752074658870697},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.5141268372535706},{"id":"https://openalex.org/keywords/alignment-free-sequence-analysis","display_name":"Alignment-free sequence analysis","score":0.49387484788894653},{"id":"https://openalex.org/keywords/hidden-markov-model","display_name":"Hidden Markov model","score":0.4851313531398773},{"id":"https://openalex.org/keywords/computational-statistics","display_name":"Computational statistics","score":0.46545249223709106},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.46431538462638855},{"id":"https://openalex.org/keywords/centroid","display_name":"Centroid","score":0.46126610040664673},{"id":"https://openalex.org/keywords/markov-chain-monte-carlo","display_name":"Markov chain Monte Carlo","score":0.44471266865730286},{"id":"https://openalex.org/keywords/smith\u2013waterman-algorithm","display_name":"Smith\u2013Waterman algorithm","score":0.4437779188156128},{"id":"https://openalex.org/keywords/markov-chain","display_name":"Markov chain","score":0.43590080738067627},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.4351482391357422},{"id":"https://openalex.org/keywords/structural-alignment","display_name":"Structural alignment","score":0.42737478017807007},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.42611730098724365},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4237910211086273},{"id":"https://openalex.org/keywords/statistical-model","display_name":"Statistical model","score":0.4156445264816284},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.38884487748146057},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.26984652876853943},{"id":"https://openalex.org/keywords/bayesian-probability","display_name":"Bayesian probability","score":0.19200393557548523}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7576150894165039},{"id":"https://openalex.org/C88031987","wikidata":"https://www.wikidata.org/wiki/Q1377767","display_name":"Multiple sequence alignment","level":5,"score":0.752074658870697},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.5141268372535706},{"id":"https://openalex.org/C180384323","wikidata":"https://www.wikidata.org/wiki/Q16335137","display_name":"Alignment-free sequence analysis","level":5,"score":0.49387484788894653},{"id":"https://openalex.org/C23224414","wikidata":"https://www.wikidata.org/wiki/Q176769","display_name":"Hidden Markov model","level":2,"score":0.4851313531398773},{"id":"https://openalex.org/C176222170","wikidata":"https://www.wikidata.org/wiki/Q5157340","display_name":"Computational statistics","level":2,"score":0.46545249223709106},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.46431538462638855},{"id":"https://openalex.org/C146599234","wikidata":"https://www.wikidata.org/wiki/Q511093","display_name":"Centroid","level":2,"score":0.46126610040664673},{"id":"https://openalex.org/C111350023","wikidata":"https://www.wikidata.org/wiki/Q1191869","display_name":"Markov chain Monte Carlo","level":3,"score":0.44471266865730286},{"id":"https://openalex.org/C72802188","wikidata":"https://www.wikidata.org/wiki/Q1683352","display_name":"Smith\u2013Waterman algorithm","level":5,"score":0.4437779188156128},{"id":"https://openalex.org/C98763669","wikidata":"https://www.wikidata.org/wiki/Q176645","display_name":"Markov chain","level":2,"score":0.43590080738067627},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.4351482391357422},{"id":"https://openalex.org/C4668613","wikidata":"https://www.wikidata.org/wiki/Q4116110","display_name":"Structural alignment","level":5,"score":0.42737478017807007},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.42611730098724365},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4237910211086273},{"id":"https://openalex.org/C114289077","wikidata":"https://www.wikidata.org/wiki/Q3284399","display_name":"Statistical model","level":2,"score":0.4156445264816284},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.38884487748146057},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.26984652876853943},{"id":"https://openalex.org/C107673813","wikidata":"https://www.wikidata.org/wiki/Q812534","display_name":"Bayesian probability","level":2,"score":0.19200393557548523},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.0},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","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":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","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":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003627","descriptor_name":"Data Interpretation, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003627","descriptor_name":"Data Interpretation, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003627","descriptor_name":"Data Interpretation, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012680","descriptor_name":"Sensitivity and Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012680","descriptor_name":"Sensitivity and Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012680","descriptor_name":"Sensitivity and Specificity","qualifier_ui":null,"qualifier_name":null,"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":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017421","descriptor_name":"Sequence Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017421","descriptor_name":"Sequence Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017421","descriptor_name":"Sequence Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":7,"locations":[{"id":"doi:10.1371/journal.pcbi.1000392","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1000392","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1000392&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},{"id":"pmid:19478997","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/19478997","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":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:authors.library.caltech.edu:74800","is_oa":true,"landing_page_url":"https://authors.library.caltech.edu/74800/","pdf_url":null,"source":{"id":"https://openalex.org/S4306402161","display_name":"CaltechAUTHORS (California Institute of Technology)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I122411786","host_organization_name":"California Institute of Technology","host_organization_lineage":["https://openalex.org/I122411786"],"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":"","raw_type":"Article"},{"id":"pmh:oai:RePEc:plo:pcbi00:1000392","is_oa":false,"landing_page_url":"https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1000392","pdf_url":null,"source":{"id":"https://openalex.org/S4306401271","display_name":"RePEc: Research Papers in Economics","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I77793887","host_organization_name":"Federal Reserve Bank of St. Louis","host_organization_lineage":["https://openalex.org/I77793887"],"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":"article"},{"id":"pmh:oai:doaj.org/article:e3b9454ac68745d18b7a4d98c31e59bf","is_oa":true,"landing_page_url":"https://doaj.org/article/e3b9454ac68745d18b7a4d98c31e59bf","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 5, Iss 5, p e1000392 (2009)","raw_type":"article"},{"id":"pmh:oai:figshare.com:article/147425","is_oa":true,"landing_page_url":"https://figshare.com/articles/dataset/Fast_Statistical_Alignment/147425","pdf_url":null,"source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"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":"","raw_type":"Dataset"},{"id":"pmh:oai:pubmedcentral.nih.gov:2684580","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2684580","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":"PLoS Comput Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1000392","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1000392","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1000392&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1272981243","display_name":null,"funder_award_id":"CCF 03-47992","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G6671297155","display_name":null,"funder_award_id":"CAREER","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"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/F4320337348","display_name":"National Human Genome Research Institute","ror":"https://ror.org/00baak391"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2011289056.pdf","grobid_xml":"https://content.openalex.org/works/W2011289056.grobid-xml"},"referenced_works_count":75,"referenced_works":["https://openalex.org/W107339557","https://openalex.org/W1480049974","https://openalex.org/W1509333633","https://openalex.org/W1519266993","https://openalex.org/W1522740115","https://openalex.org/W1525734744","https://openalex.org/W1549024371","https://openalex.org/W1557399695","https://openalex.org/W1767772592","https://openalex.org/W1968256798","https://openalex.org/W1988925586","https://openalex.org/W1996386189","https://openalex.org/W1997631042","https://openalex.org/W1999707793","https://openalex.org/W2009570821","https://openalex.org/W2017777683","https://openalex.org/W2024665422","https://openalex.org/W2033339460","https://openalex.org/W2042881722","https://openalex.org/W2052831012","https://openalex.org/W2054624670","https://openalex.org/W2066502527","https://openalex.org/W2067150932","https://openalex.org/W2067579500","https://openalex.org/W2069787595","https://openalex.org/W2073234837","https://openalex.org/W2084763084","https://openalex.org/W2092979861","https://openalex.org/W2095824228","https://openalex.org/W2099762535","https://openalex.org/W2104729238","https://openalex.org/W2106882534","https://openalex.org/W2107282968","https://openalex.org/W2107511706","https://openalex.org/W2112132489","https://openalex.org/W2115711269","https://openalex.org/W2117804170","https://openalex.org/W2118829610","https://openalex.org/W2119362018","https://openalex.org/W2121691652","https://openalex.org/W2124627199","https://openalex.org/W2126332379","https://openalex.org/W2126753236","https://openalex.org/W2127164334","https://openalex.org/W2127688908","https://openalex.org/W2128599049","https://openalex.org/W2130043776","https://openalex.org/W2136570298","https://openalex.org/W2137015675","https://openalex.org/W2139243714","https://openalex.org/W2140872496","https://openalex.org/W2142113273","https://openalex.org/W2143292980","https://openalex.org/W2143357251","https://openalex.org/W2144362290","https://openalex.org/W2144767153","https://openalex.org/W2144775551","https://openalex.org/W2146974293","https://openalex.org/W2147847662","https://openalex.org/W2148047088","https://openalex.org/W2151120398","https://openalex.org/W2155237411","https://openalex.org/W2159235552","https://openalex.org/W2161292693","https://openalex.org/W2163798335","https://openalex.org/W2165686834","https://openalex.org/W2166718648","https://openalex.org/W2170765088","https://openalex.org/W2243001382","https://openalex.org/W2610493105","https://openalex.org/W3164276917","https://openalex.org/W3199943451","https://openalex.org/W4245668478","https://openalex.org/W6986512933","https://openalex.org/W6988022094"],"related_works":["https://openalex.org/W2051969447","https://openalex.org/W2468116983","https://openalex.org/W2111937814","https://openalex.org/W2948014085","https://openalex.org/W1486249959","https://openalex.org/W1482324242","https://openalex.org/W2029514038","https://openalex.org/W2141411672","https://openalex.org/W2103737249","https://openalex.org/W2122131968"],"abstract_inverted_index":{"We":[0],"describe":[1],"a":[2,45,49,63,174,187],"new":[3],"program":[4,31,172],"for":[5,20,87,122,178],"the":[6,55,82,93,154,193],"alignment":[7,83,98,141,158],"of":[8,81,92,111,156],"multiple":[9,64,74],"biological":[10,160],"sequences":[11],"that":[12,23,165],"is":[13,32,196],"both":[14],"statistically":[15],"motivated":[16],"and":[17,47,85,90,173,192],"fast":[18],"enough":[19],"problem":[21],"sizes":[22],"arise":[24],"in":[25,134,146,162,181],"practice.":[26],"Our":[27],"Fast":[28],"Statistical":[29],"Alignment":[30],"based":[33],"on":[34,44,130,159],"pair":[35],"hidden":[36],"Markov":[37,103],"models":[38,61],"which":[39,76,100,125],"approximate":[40],"an":[41,117],"insertion/deletion":[42],"process":[43],"tree":[46],"uses":[48,67],"sequence":[50],"annealing":[51],"algorithm":[52],"to":[53,72,127,136,164],"combine":[54],"posterior":[56],"probabilities":[57],"estimated":[58],"from":[59],"these":[60],"into":[62],"alignment.":[65],"FSA":[66,115,171],"its":[68,149],"explicit":[69],"statistical":[70],"model":[71],"produce":[73],"alignments":[75,133,182],"are":[77],"accompanied":[78],"by":[79,144,167],"estimates":[80],"accuracy":[84,129],"uncertainty":[86,180],"every":[88],"column":[89],"character":[91],"alignment--previously":[94],"available":[95,197],"only":[96],"with":[97,148],"programs":[99],"use":[101],"computationally-expensive":[102],"Chain":[104],"Monte":[105],"Carlo":[106],"approaches--yet":[107],"can":[108,183],"align":[109],"thousands":[110],"long":[112],"sequences.":[113],"Moreover,":[114],"utilizes":[116],"unsupervised":[118],"query-specific":[119],"learning":[120,150],"procedure":[121],"parameter":[123],"estimation":[124],"leads":[126],"improved":[128],"benchmark":[131],"reference":[132],"comparison":[135,163],"existing":[137],"programs.":[138],"The":[139,170],"centroid":[140],"approach":[142],"taken":[143],"FSA,":[145],"combination":[147],"procedure,":[151],"drastically":[152],"reduces":[153],"amount":[155],"false-positive":[157],"data":[161],"given":[166],"other":[168],"methods.":[169],"companion":[175],"visualization":[176],"tool":[177],"exploring":[179],"be":[184],"used":[185],"via":[186],"web":[188],"interface":[189],"at":[190,198],"http://orangutan.math.berkeley.edu/fsa/,":[191],"source":[194],"code":[195],"http://fsa.sourceforge.net/.":[199]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":9},{"year":2024,"cited_by_count":20},{"year":2023,"cited_by_count":11},{"year":2022,"cited_by_count":11},{"year":2021,"cited_by_count":13},{"year":2020,"cited_by_count":21},{"year":2019,"cited_by_count":25},{"year":2018,"cited_by_count":27},{"year":2017,"cited_by_count":22},{"year":2016,"cited_by_count":27},{"year":2015,"cited_by_count":27},{"year":2014,"cited_by_count":24},{"year":2013,"cited_by_count":28},{"year":2012,"cited_by_count":41}],"updated_date":"2026-04-24T08:23:43.765630","created_date":"2025-10-10T00:00:00"}
