{"id":"https://openalex.org/W1773019931","doi":"https://doi.org/10.1186/1471-2105-7-265","title":"A jumping profile Hidden Markov Model and applications to recombination sites in HIV and HCV genomes","display_name":"A jumping profile Hidden Markov Model and applications to recombination sites in HIV and HCV genomes","publication_year":2006,"publication_date":"2006-05-22","ids":{"openalex":"https://openalex.org/W1773019931","doi":"https://doi.org/10.1186/1471-2105-7-265","mag":"1773019931","pmid":"https://pubmed.ncbi.nlm.nih.gov/16716226"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-7-265","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-7-265","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-7-265","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"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":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-7-265","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5015651328","display_name":"Anne-Kathrin Schultz","orcid":"https://orcid.org/0000-0002-0963-4275"},"institutions":[{"id":"https://openalex.org/I74656192","display_name":"University of G\u00f6ttingen","ror":"https://ror.org/01y9bpm73","country_code":"DE","type":"education","lineage":["https://openalex.org/I74656192"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Anne-Kathrin Schultz","raw_affiliation_strings":["Institute of Microbiology and Genetics, University of G\u00f6ttingen, Goldschmidtstr, 1, 37077 G\u00f6ttingen, Germany. aschult2@gwdg.de","Institute of Microbiology and Genetics, University of G\u00f6ttingen, G\u00f6ttingen, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Microbiology and Genetics, University of G\u00f6ttingen, Goldschmidtstr, 1, 37077 G\u00f6ttingen, Germany. aschult2@gwdg.de","institution_ids":["https://openalex.org/I74656192"]},{"raw_affiliation_string":"Institute of Microbiology and Genetics, University of G\u00f6ttingen, G\u00f6ttingen, Germany","institution_ids":["https://openalex.org/I74656192"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100447315","display_name":"Ming Zhang","orcid":"https://orcid.org/0000-0003-1175-4636"},"institutions":[{"id":"https://openalex.org/I1343871089","display_name":"Los Alamos National Laboratory","ror":"https://ror.org/01e41cf67","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I1343871089","https://openalex.org/I198811213","https://openalex.org/I4210120050"]},{"id":"https://openalex.org/I74656192","display_name":"University of G\u00f6ttingen","ror":"https://ror.org/01y9bpm73","country_code":"DE","type":"education","lineage":["https://openalex.org/I74656192"]}],"countries":["DE","US"],"is_corresponding":false,"raw_author_name":"Ming Zhang","raw_affiliation_strings":["Institute of Microbiology and Genetics, University of G\u00f6ttingen, Goldschmidtstr. 1, 37077, G\u00f6ttingen, Germany","Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA","Institute of Microbiology and Genetics, University of G\u00f6ttingen, G\u00f6ttingen, Germany","Theoretical Division, Los Alamos National Laboratory, Los Alamos, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Microbiology and Genetics, University of G\u00f6ttingen, Goldschmidtstr. 1, 37077, G\u00f6ttingen, Germany","institution_ids":["https://openalex.org/I74656192"]},{"raw_affiliation_string":"Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA","institution_ids":["https://openalex.org/I1343871089"]},{"raw_affiliation_string":"Institute of Microbiology and Genetics, University of G\u00f6ttingen, G\u00f6ttingen, Germany","institution_ids":["https://openalex.org/I74656192"]},{"raw_affiliation_string":"Theoretical Division, Los Alamos National Laboratory, Los Alamos, USA","institution_ids":["https://openalex.org/I1343871089"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023859958","display_name":"Thomas Leitner","orcid":"https://orcid.org/0000-0001-8160-2588"},"institutions":[{"id":"https://openalex.org/I1343871089","display_name":"Los Alamos National Laboratory","ror":"https://ror.org/01e41cf67","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I1343871089","https://openalex.org/I198811213","https://openalex.org/I4210120050"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Thomas Leitner","raw_affiliation_strings":["Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA","Theoretical Division , Los Alamos National Laboratory , Los Alamos, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA","institution_ids":["https://openalex.org/I1343871089"]},{"raw_affiliation_string":"Theoretical Division , Los Alamos National Laboratory , Los Alamos, USA","institution_ids":["https://openalex.org/I1343871089"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5045816128","display_name":"Carla Kuiken","orcid":null},"institutions":[{"id":"https://openalex.org/I1343871089","display_name":"Los Alamos National Laboratory","ror":"https://ror.org/01e41cf67","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I1343871089","https://openalex.org/I198811213","https://openalex.org/I4210120050"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Carla Kuiken","raw_affiliation_strings":["Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA","Theoretical Division , Los Alamos National Laboratory , Los Alamos, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA","institution_ids":["https://openalex.org/I1343871089"]},{"raw_affiliation_string":"Theoretical Division , Los Alamos National Laboratory , Los Alamos, USA","institution_ids":["https://openalex.org/I1343871089"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022985881","display_name":"Bette Korber","orcid":"https://orcid.org/0000-0002-2026-5757"},"institutions":[{"id":"https://openalex.org/I1308548392","display_name":"Santa Fe Institute","ror":"https://ror.org/01arysc35","country_code":"US","type":"funder","lineage":["https://openalex.org/I1308548392"]},{"id":"https://openalex.org/I1343871089","display_name":"Los Alamos National Laboratory","ror":"https://ror.org/01e41cf67","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I1343871089","https://openalex.org/I198811213","https://openalex.org/I4210120050"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Bette Korber","raw_affiliation_strings":["The Santa Fe Institute, Santa Fe, NM, 87501, USA","Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA","The Santa Fe Institute, Santa Fe","Theoretical Division, Los Alamos National Laboratory, Los Alamos, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Santa Fe Institute, Santa Fe, NM, 87501, USA","institution_ids":["https://openalex.org/I1308548392"]},{"raw_affiliation_string":"Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA","institution_ids":["https://openalex.org/I1343871089"]},{"raw_affiliation_string":"The Santa Fe Institute, Santa Fe","institution_ids":["https://openalex.org/I1308548392"]},{"raw_affiliation_string":"Theoretical Division, Los Alamos National Laboratory, Los Alamos, USA","institution_ids":["https://openalex.org/I1343871089"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024220352","display_name":"Burkhard Morgenstern","orcid":"https://orcid.org/0000-0002-7431-2862"},"institutions":[{"id":"https://openalex.org/I74656192","display_name":"University of G\u00f6ttingen","ror":"https://ror.org/01y9bpm73","country_code":"DE","type":"education","lineage":["https://openalex.org/I74656192"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Burkhard Morgenstern","raw_affiliation_strings":["Institute of Microbiology and Genetics, University of G\u00f6ttingen, Goldschmidtstr. 1, 37077, G\u00f6ttingen, Germany","Institute of Microbiology and Genetics, University of G\u00f6ttingen, G\u00f6ttingen, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Microbiology and Genetics, University of G\u00f6ttingen, Goldschmidtstr. 1, 37077, G\u00f6ttingen, Germany","institution_ids":["https://openalex.org/I74656192"]},{"raw_affiliation_string":"Institute of Microbiology and Genetics, University of G\u00f6ttingen, G\u00f6ttingen, Germany","institution_ids":["https://openalex.org/I74656192"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5025051195","display_name":"Mario Stanke","orcid":"https://orcid.org/0000-0001-8696-0384"},"institutions":[{"id":"https://openalex.org/I74656192","display_name":"University of G\u00f6ttingen","ror":"https://ror.org/01y9bpm73","country_code":"DE","type":"education","lineage":["https://openalex.org/I74656192"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Mario Stanke","raw_affiliation_strings":["Institute of Microbiology and Genetics, University of G\u00f6ttingen, Goldschmidtstr. 1, 37077, G\u00f6ttingen, Germany","Institute of Microbiology and Genetics, University of G\u00f6ttingen, G\u00f6ttingen, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Microbiology and Genetics, University of G\u00f6ttingen, Goldschmidtstr. 1, 37077, G\u00f6ttingen, Germany","institution_ids":["https://openalex.org/I74656192"]},{"raw_affiliation_string":"Institute of Microbiology and Genetics, University of G\u00f6ttingen, G\u00f6ttingen, Germany","institution_ids":["https://openalex.org/I74656192"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5025051195"],"corresponding_institution_ids":["https://openalex.org/I74656192"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":2.1609,"has_fulltext":true,"cited_by_count":104,"citation_normalized_percentile":{"value":0.86126292,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"7","issue":"1","first_page":"265","last_page":"265"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.725600004196167,"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":0.725600004196167,"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/T12946","display_name":"Fractal and DNA sequence analysis","score":0.05130000039935112,"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":0.014600000344216824,"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/hidden-markov-model","display_name":"Hidden Markov model","score":0.6144172549247742},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.5902681946754456},{"id":"https://openalex.org/keywords/human-immunodeficiency-virus","display_name":"Human immunodeficiency virus (HIV)","score":0.5743697881698608},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5594731569290161},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.5165299773216248},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4996657371520996},{"id":"https://openalex.org/keywords/virology","display_name":"Virology","score":0.47647330164909363},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.45840054750442505},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.37722763419151306},{"id":"https://openalex.org/keywords/evolutionary-biology","display_name":"Evolutionary biology","score":0.32969745993614197},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.226558655500412},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.17729324102401733},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.08192417025566101}],"concepts":[{"id":"https://openalex.org/C23224414","wikidata":"https://www.wikidata.org/wiki/Q176769","display_name":"Hidden Markov model","level":2,"score":0.6144172549247742},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.5902681946754456},{"id":"https://openalex.org/C3013748606","wikidata":"https://www.wikidata.org/wiki/Q15787","display_name":"Human immunodeficiency virus (HIV)","level":2,"score":0.5743697881698608},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5594731569290161},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.5165299773216248},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4996657371520996},{"id":"https://openalex.org/C159047783","wikidata":"https://www.wikidata.org/wiki/Q7215","display_name":"Virology","level":1,"score":0.47647330164909363},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.45840054750442505},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.37722763419151306},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.32969745993614197},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.226558655500412},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.17729324102401733},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.08192417025566101}],"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":"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":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","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":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011995","descriptor_name":"Recombination, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011995","descriptor_name":"Recombination, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011995","descriptor_name":"Recombination, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015497","descriptor_name":"HIV-1","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D015497","descriptor_name":"HIV-1","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D015497","descriptor_name":"HIV-1","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D015497","descriptor_name":"HIV-1","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015497","descriptor_name":"HIV-1","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015497","descriptor_name":"HIV-1","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016174","descriptor_name":"Hepacivirus","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D016174","descriptor_name":"Hepacivirus","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D016174","descriptor_name":"Hepacivirus","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D016174","descriptor_name":"Hepacivirus","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016174","descriptor_name":"Hepacivirus","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016174","descriptor_name":"Hepacivirus","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016679","descriptor_name":"Genome, Viral","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016679","descriptor_name":"Genome, Viral","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016679","descriptor_name":"Genome, Viral","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030561","descriptor_name":"Databases, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030561","descriptor_name":"Databases, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030561","descriptor_name":"Databases, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":8,"locations":[{"id":"doi:10.1186/1471-2105-7-265","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-7-265","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-7-265","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"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":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:16716226","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/16716226","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:osti.gov:1626321","is_oa":true,"landing_page_url":"https://www.osti.gov/biblio/1626321","pdf_url":"https://www.osti.gov/servlets/purl/1626321","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:doaj.org/article:70cd7d1c848d444eb1d2c003dffbf1ee","is_oa":true,"landing_page_url":"https://doaj.org/article/70cd7d1c848d444eb1d2c003dffbf1ee","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":"BMC Bioinformatics, Vol 7, Iss 1, p 265 (2006)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:1336269","is_oa":true,"landing_page_url":"http://europepmc.org/articles/PMC1525204","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":"Text"},{"id":"pmh:oai:goescholar:1/4407","is_oa":true,"landing_page_url":"http://resolver.sub.uni-goettingen.de/purl?gs-1/4407","pdf_url":null,"source":{"id":"https://openalex.org/S4306401634","display_name":"GoeScholar  The Publication Server of the Georg-August-Universit\u00e4t G\u00f6ttingen (Georg-August-Universit\u00e4t G\u00f6ttingen)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210122495","host_organization_name":"Asklepios Klinik St. Georg","host_organization_lineage":["https://openalex.org/I4210122495"],"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":"journalArticle"},{"id":"pmh:oai:publications.goettingen-research-online.de:2/35357","is_oa":true,"landing_page_url":"https://resolver.sub.uni-goettingen.de/purl?gro-2/35357","pdf_url":null,"source":{"id":"https://openalex.org/S4306401634","display_name":"GoeScholar  The Publication Server of the Georg-August-Universit\u00e4t G\u00f6ttingen (Georg-August-Universit\u00e4t G\u00f6ttingen)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210122495","host_organization_name":"Asklepios Klinik St. Georg","host_organization_lineage":["https://openalex.org/I4210122495"],"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":"journal_article"},{"id":"pmh:oai:pubmedcentral.nih.gov:1525204","is_oa":true,"landing_page_url":"http://doi.org/10.1186/1471-2105-7-265","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":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-7-265","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-7-265","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-7-265","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"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":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Good health and well-being","score":0.8399999737739563,"id":"https://metadata.un.org/sdg/3"}],"awards":[{"id":"https://openalex.org/G1450082238","display_name":null,"funder_award_id":"Y01 AI001500","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"},{"id":"https://openalex.org/G6170584815","display_name":null,"funder_award_id":"Y1-AI-1500-01","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"}],"funders":[{"id":"https://openalex.org/F4320306084","display_name":"U.S. Department of Energy","ror":"https://ror.org/01bj3aw27"},{"id":"https://openalex.org/F4320320879","display_name":"Deutsche Forschungsgemeinschaft","ror":"https://ror.org/018mejw64"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337355","display_name":"National Institute of Allergy and Infectious Diseases","ror":"https://ror.org/043z4tv69"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1773019931.pdf","grobid_xml":"https://content.openalex.org/works/W1773019931.grobid-xml"},"referenced_works_count":40,"referenced_works":["https://openalex.org/W1791996297","https://openalex.org/W1969696464","https://openalex.org/W1974441274","https://openalex.org/W1990096140","https://openalex.org/W1991133427","https://openalex.org/W1992471261","https://openalex.org/W1992926970","https://openalex.org/W2002468303","https://openalex.org/W2007735554","https://openalex.org/W2039567452","https://openalex.org/W2045790346","https://openalex.org/W2052831012","https://openalex.org/W2055043387","https://openalex.org/W2058949165","https://openalex.org/W2059513540","https://openalex.org/W2061192306","https://openalex.org/W2070324371","https://openalex.org/W2071464831","https://openalex.org/W2077103006","https://openalex.org/W2085399039","https://openalex.org/W2086745360","https://openalex.org/W2087757756","https://openalex.org/W2091181646","https://openalex.org/W2102122585","https://openalex.org/W2109179288","https://openalex.org/W2113037857","https://openalex.org/W2122665495","https://openalex.org/W2135350300","https://openalex.org/W2137095888","https://openalex.org/W2140136392","https://openalex.org/W2143334889","https://openalex.org/W2149238618","https://openalex.org/W2151831732","https://openalex.org/W2158666214","https://openalex.org/W2158710467","https://openalex.org/W2163400707","https://openalex.org/W2172811609","https://openalex.org/W3147254695","https://openalex.org/W3214380909","https://openalex.org/W4245668478"],"related_works":["https://openalex.org/W2053269318","https://openalex.org/W2364370872","https://openalex.org/W2097963413","https://openalex.org/W2025614924","https://openalex.org/W2294335174","https://openalex.org/W3145575561","https://openalex.org/W2995886640","https://openalex.org/W1591475660","https://openalex.org/W2001275470","https://openalex.org/W2164162849"],"abstract_inverted_index":{"BACKGROUND:":[0],"Jumping":[1],"alignments":[2],"have":[3],"recently":[4],"been":[5],"proposed":[6],"as":[7,34,167,169],"a":[8,12,19,24,35,87,94,102,134,151],"strategy":[9],"to":[10,28,42,66,121,133,150,170,188,197,211],"search":[11],"given":[13],"multiple":[14,30,72],"sequence":[15,26,108,112],"alignment":[16,31],"A":[17],"against":[18],"database.":[20],"Instead":[21],"of":[22,61,97,104,143,154],"comparing":[23,224],"database":[25,135],"S":[27,37,50,62],"the":[29,70,98,105],"or":[32],"profile":[33,89,184],"whole,":[36],"is":[38,76,129],"compared":[39],"and":[40,162],"aligned":[41,65,106],"individual":[43],"sequences":[44,55,68,156],"from":[45,56,69,157],"A.":[46],"Within":[47],"this":[48],"alignment,":[49],"can":[51,63,116,193],"jump":[52,117],"between":[53,118,138],"different":[54,59,67,123,139],"A,":[57],"so":[58],"parts":[60],"be":[64,195,212],"input":[71,107],"alignment.":[73],"This":[74],"approach":[75,192],"particularly":[77],"useful":[78],"for":[79],"dealing":[80],"with":[81],"recombination":[82,189,204],"events.":[83],"RESULTS:":[84],"We":[85,146],"developed":[86],"jumping":[88,183],"Hidden":[90],"Markov":[91],"Model":[92],"(jpHMM),":[93],"probabilistic":[95],"generalization":[96],"jumping-alignment":[99],"approach.":[100],"Given":[101],"partition":[103],"family":[109],"into":[110],"known":[111],"subtypes,":[113,124],"our":[114,148,182,191],"model":[115],"states":[119],"corresponding":[120],"these":[122],"depending":[125],"on":[126,223],"which":[127],"subtype":[128],"locally":[130],"most":[131],"similar":[132],"sequence.":[136],"Jumps":[137],"subtypes":[140],"are":[141],"indicative":[142],"intersubtype":[144],"recombinations.":[145],"applied":[147],"method":[149],"large":[152],"set":[153],"genome":[155,173],"human":[158],"immunodeficiency":[159],"virus":[160,165],"(HIV)":[161],"hepatitis":[163],"C":[164],"(HCV)":[166],"well":[168],"simulated":[171],"recombined":[172],"sequences.":[174,202,227],"CONCLUSION:":[175],"Our":[176],"results":[177],"demonstrate":[178],"that":[179],"jumps":[180],"in":[181,200],"HMM":[185],"often":[186],"correspond":[187],"breakpoints;":[190],"therefore":[194],"used":[196],"detect":[198],"recombinations":[199],"genomic":[201],"The":[203],"breakpoints":[205,217],"identified":[206],"by":[207,219],"jpHMM":[208],"were":[209],"found":[210],"significantly":[213],"more":[214],"accurate":[215],"than":[216],"defined":[218],"traditional":[220],"methods":[221],"based":[222],"single":[225],"representative":[226]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":5},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":4},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":8},{"year":2015,"cited_by_count":3},{"year":2014,"cited_by_count":11},{"year":2013,"cited_by_count":5},{"year":2012,"cited_by_count":16}],"updated_date":"2026-07-29T09:40:50.615796","created_date":"2025-10-10T00:00:00"}