Improved Algorithmic Complexity for the 3SEQ Recombination Detection Algorithm
Abstract Identifying recombinant sequences in an era of large genomic databases is challenging as it requires an efficient algorithm to identify candidate recombinants and parents, as well as appropriate statistical methods to correct for the large number of comparisons performed. In 2007, a computa...
Gespeichert in:
| Veröffentlicht in: | Molecular biology and evolution Jg. 35; H. 1; S. 247 - 251 |
|---|---|
| Hauptverfasser: | , , |
| Format: | Journal Article |
| Sprache: | Englisch |
| Veröffentlicht: |
United States
Oxford University Press
01.01.2018
|
| Schlagworte: | |
| ISSN: | 0737-4038, 1537-1719, 1537-1719 |
| Online-Zugang: | Volltext |
| Tags: |
Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
|
| Abstract | Abstract
Identifying recombinant sequences in an era of large genomic databases is challenging as it requires an efficient algorithm to identify candidate recombinants and parents, as well as appropriate statistical methods to correct for the large number of comparisons performed. In 2007, a computation was introduced for an exact nonparametric mosaicism statistic that gave high-precision P values for putative recombinants. This exact computation meant that multiple-comparisons corrected P values also had high precision, which is crucial when performing millions or billions of tests in large databases. Here, we introduce an improvement to the algorithmic complexity of this computation from O(mn3) to O(mn2), where m and n are the numbers of recombination-informative sites in the candidate recombinant. This new computation allows for recombination analysis to be performed in alignments with thousands of polymorphic sites. Benchmark runs are presented on viral genome sequence alignments, new features are introduced, and applications outside recombination analysis are discussed. |
|---|---|
| AbstractList | Identifying recombinant sequences in an era of large genomic databases is challenging as it requires an efficient algorithm to identify candidate recombinants and parents, as well as appropriate statistical methods to correct for the large number of comparisons performed. In 2007, a computation was introduced for an exact nonparametric mosaicism statistic that gave high-precision P values for putative recombinants. This exact computation meant that multiple-comparisons corrected P values also had high precision, which is crucial when performing millions or billions of tests in large databases. Here, we introduce an improvement to the algorithmic complexity of this computation from O(mn3) to O(mn2), where m and n are the numbers of recombination-informative sites in the candidate recombinant. This new computation allows for recombination analysis to be performed in alignments with thousands of polymorphic sites. Benchmark runs are presented on viral genome sequence alignments, new features are introduced, and applications outside recombination analysis are discussed. Abstract Identifying recombinant sequences in an era of large genomic databases is challenging as it requires an efficient algorithm to identify candidate recombinants and parents, as well as appropriate statistical methods to correct for the large number of comparisons performed. In 2007, a computation was introduced for an exact nonparametric mosaicism statistic that gave high-precision P values for putative recombinants. This exact computation meant that multiple-comparisons corrected P values also had high precision, which is crucial when performing millions or billions of tests in large databases. Here, we introduce an improvement to the algorithmic complexity of this computation from O(mn3) to O(mn2), where m and n are the numbers of recombination-informative sites in the candidate recombinant. This new computation allows for recombination analysis to be performed in alignments with thousands of polymorphic sites. Benchmark runs are presented on viral genome sequence alignments, new features are introduced, and applications outside recombination analysis are discussed. Identifying recombinant sequences in an era of large genomic databases is challenging as it requires an efficient algorithm to identify candidate recombinants and parents, as well as appropriate statistical methods to correct for the large number of comparisons performed. In 2007, a computation was introduced for an exact nonparametric mosaicism statistic that gave high-precision P values for putative recombinants. This exact computation meant that multiple-comparisons corrected P values also had high precision, which is crucial when performing millions or billions of tests in large databases. Here, we introduce an improvement to the algorithmic complexity of this computation from O(mn3) to O(mn2), where m and n are the numbers of recombination-informative sites in the candidate recombinant. This new computation allows for recombination analysis to be performed in alignments with thousands of polymorphic sites. Benchmark runs are presented on viral genome sequence alignments, new features are introduced, and applications outside recombination analysis are discussed.Identifying recombinant sequences in an era of large genomic databases is challenging as it requires an efficient algorithm to identify candidate recombinants and parents, as well as appropriate statistical methods to correct for the large number of comparisons performed. In 2007, a computation was introduced for an exact nonparametric mosaicism statistic that gave high-precision P values for putative recombinants. This exact computation meant that multiple-comparisons corrected P values also had high precision, which is crucial when performing millions or billions of tests in large databases. Here, we introduce an improvement to the algorithmic complexity of this computation from O(mn3) to O(mn2), where m and n are the numbers of recombination-informative sites in the candidate recombinant. This new computation allows for recombination analysis to be performed in alignments with thousands of polymorphic sites. Benchmark runs are presented on viral genome sequence alignments, new features are introduced, and applications outside recombination analysis are discussed. |
| Author | Lam, Ha Minh Boni, Maciej F Ratmann, Oliver |
| AuthorAffiliation | 4 Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, University Park, PA 3 MRC Centre for Outbreak Analyses and Modelling, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom 2 Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom 1 Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam |
| AuthorAffiliation_xml | – name: 2 Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom – name: 3 MRC Centre for Outbreak Analyses and Modelling, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom – name: 1 Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam – name: 4 Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, University Park, PA |
| Author_xml | – sequence: 1 givenname: Ha Minh surname: Lam fullname: Lam, Ha Minh organization: Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam – sequence: 2 givenname: Oliver surname: Ratmann fullname: Ratmann, Oliver organization: MRC Centre for Outbreak Analyses and Modelling, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom – sequence: 3 givenname: Maciej F surname: Boni fullname: Boni, Maciej F email: mfb9@psu.edu organization: Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/29029186$$D View this record in MEDLINE/PubMed |
| BookMark | eNqFkc1rFTEUxYNU7Gvr0q0MuHEzNl-TTDZCeVYtFItW1yGTd6cvZTIZk8yj_e9N-16LFqSrXMjvHM659wDtjWEEhN4Q_IFgxY59GDrYHPt0QwV7gRakYbImkqg9tMCyzByzdh8dpHSNMeFciFdonypMFWnFAn0781MMG1hVJ8NViC6vvbPVMvhpgBuXb6s-xCqvoWKXp9-rH2CD79xosgtj9Qky2PvpUXuEXvZmSPB69x6iX59Pfy6_1ucXX86WJ-e1bTjN9YpKQ7teWMzoijFOWctFKyR0YJiyHTOmEyWfAmiowS1I3vRGguDW0hYDO0Qft77T3HlYWRhzNIOeovMm3upgnP73Z3RrfRU2ummbu-rF4P3OIIbfM6SsvUsWhsGMEOakiWoIJ1I1oqDvnqDXYY5jqacZkVhhIgUu1Nu_Ez1GeVh1AdgWsDGkFKHX1uX7RZaAbtAE67uD6u1B9fagRVU_UT0Y_4_f9Qrz9Az6B_Q8tEE |
| CitedBy_id | crossref_primary_10_3390_microorganisms11040983 crossref_primary_10_3390_pathogens14030233 crossref_primary_10_3390_genes13050909 crossref_primary_10_3390_v14051095 crossref_primary_10_1128_msystems_00246_20 crossref_primary_10_1186_s12915_020_00839_8 crossref_primary_10_1016_j_meegid_2019_104058 crossref_primary_10_1016_j_meegid_2020_104467 crossref_primary_10_3390_pathogens10020180 crossref_primary_10_1093_ve_veac054 crossref_primary_10_1016_j_cell_2021_08_014 crossref_primary_10_3390_v12101096 crossref_primary_10_1007_s42991_024_00433_3 crossref_primary_10_3390_v14102125 crossref_primary_10_3390_v16010046 crossref_primary_10_1038_s41564_020_0771_4 crossref_primary_10_1128_spectrum_04071_23 crossref_primary_10_1111_1462_2920_16665 crossref_primary_10_3389_fmicb_2021_699078 crossref_primary_10_1016_j_cell_2019_07_038 crossref_primary_10_1016_j_micpath_2023_106504 crossref_primary_10_3390_ijms252111702 crossref_primary_10_3390_ijms26125595 crossref_primary_10_3390_pathogens9100823 crossref_primary_10_1128_spectrum_00840_23 crossref_primary_10_3390_pathogens14080743 crossref_primary_10_3390_v14122669 crossref_primary_10_1002_jmv_28902 crossref_primary_10_1016_j_meegid_2024_105671 crossref_primary_10_1016_j_jviromet_2024_114986 crossref_primary_10_1099_mgen_0_000984 crossref_primary_10_1093_sysbio_syaa099 crossref_primary_10_1080_07060661_2019_1566179 crossref_primary_10_1038_s41467_024_46109_x crossref_primary_10_1038_s41598_021_96690_0 crossref_primary_10_3390_pathogens12050740 crossref_primary_10_1111_tbed_14356 crossref_primary_10_3390_v15061371 crossref_primary_10_1080_03079457_2023_2228725 crossref_primary_10_3390_v14092013 crossref_primary_10_1007_s10341_025_01433_4 crossref_primary_10_3389_fmicb_2022_850516 crossref_primary_10_1016_j_virs_2022_01_028 crossref_primary_10_3389_fvets_2022_987667 crossref_primary_10_1038_s41564_022_01268_9 crossref_primary_10_3390_v16040557 crossref_primary_10_1038_s41598_021_96626_8 crossref_primary_10_1038_s41598_018_27092_y crossref_primary_10_1038_s41398_022_02021_w crossref_primary_10_1186_s12985_024_02358_2 crossref_primary_10_1016_j_cell_2020_01_006 crossref_primary_10_3390_v16040560 crossref_primary_10_1371_journal_ppat_1009730 crossref_primary_10_1111_tbed_13914 crossref_primary_10_3390_v17050654 crossref_primary_10_1007_s12088_024_01191_z crossref_primary_10_3390_ijms252010878 crossref_primary_10_1016_j_psj_2025_105776 crossref_primary_10_1002_jmv_28519 crossref_primary_10_1016_j_pmpp_2021_101638 crossref_primary_10_3389_fmicb_2025_1524787 crossref_primary_10_3390_v12111313 crossref_primary_10_1093_infdis_jiac298 crossref_primary_10_3390_v17010126 crossref_primary_10_1093_bib_bbac513 crossref_primary_10_1093_sysbio_syac062 crossref_primary_10_3389_fvets_2022_846904 crossref_primary_10_1016_j_vetmic_2025_110413 crossref_primary_10_1270_jsbbs_24015 crossref_primary_10_3390_v12040427 crossref_primary_10_3390_biomedicines10092080 crossref_primary_10_3390_v12070732 crossref_primary_10_1002_advs_202505978 crossref_primary_10_1002_jmv_28653 crossref_primary_10_1016_j_psj_2023_103177 crossref_primary_10_1093_ve_veab007 crossref_primary_10_1111_1348_0421_13033 crossref_primary_10_1099_jgv_0_001572 crossref_primary_10_1016_j_virusres_2020_198077 crossref_primary_10_3390_microorganisms9050998 crossref_primary_10_3390_v17081114 crossref_primary_10_1099_mgen_0_000932 crossref_primary_10_1186_s13099_025_00740_1 crossref_primary_10_1371_journal_pntd_0010020 crossref_primary_10_1093_ve_vead066 crossref_primary_10_3390_v16010007 crossref_primary_10_3390_microorganisms10071356 crossref_primary_10_3390_v13071412 crossref_primary_10_1080_22221751_2022_2032375 crossref_primary_10_1093_ve_veab036 crossref_primary_10_3390_plants9121807 crossref_primary_10_3390_insects13090788 crossref_primary_10_3389_fmed_2022_806611 crossref_primary_10_3390_v15102132 crossref_primary_10_1093_genetics_iyab074 crossref_primary_10_1093_ve_vead051 crossref_primary_10_1038_s41467_024_51539_8 crossref_primary_10_3389_fcimb_2022_829380 crossref_primary_10_1111_nph_70120 crossref_primary_10_3390_v17070896 crossref_primary_10_1093_sysbio_syad040 crossref_primary_10_1084_jem_20180936 crossref_primary_10_1128_spectrum_03855_22 crossref_primary_10_3390_v16010096 crossref_primary_10_1016_j_vetmic_2022_109601 crossref_primary_10_1186_s12917_022_03281_w crossref_primary_10_1016_j_gpb_2023_10_004 crossref_primary_10_1126_science_abp8337 crossref_primary_10_7717_peerj_7338 crossref_primary_10_3390_vaccines9091019 crossref_primary_10_1093_molbev_msaa001 crossref_primary_10_3390_v15030743 crossref_primary_10_1093_ve_vead087 crossref_primary_10_1155_2024_2197725 crossref_primary_10_3390_v13112307 crossref_primary_10_1093_ve_veab061 crossref_primary_10_1038_s41467_022_31247_x crossref_primary_10_1093_bib_bbab107 crossref_primary_10_1186_s13567_018_0532_z crossref_primary_10_3390_d15010080 crossref_primary_10_1128_msphere_00624_23 crossref_primary_10_3390_v17060863 crossref_primary_10_1038_s41467_024_47464_5 crossref_primary_10_1016_j_micinf_2024_105304 crossref_primary_10_1186_s12985_025_02829_0 crossref_primary_10_3390_v14020440 crossref_primary_10_1038_s41561_024_01508_z crossref_primary_10_3390_ijms24032419 crossref_primary_10_1016_j_gene_2025_149252 crossref_primary_10_1007_s00705_025_06276_8 crossref_primary_10_1186_s40168_023_01619_6 crossref_primary_10_1038_s41586_022_04411_y crossref_primary_10_1038_s41467_023_39835_1 crossref_primary_10_1016_j_virusres_2020_198279 crossref_primary_10_1371_journal_pone_0260635 |
| Cites_doi | 10.1371/journal.pone.0010434 10.1534/genetics.106.068874 10.1007/s00239-001-0034-9 10.1038/nature04239 10.1099/vir.0.83122-0 10.1111/j.1755-0998.2011.03026.x 10.1093/oxfordjournals.molbev.a026121 10.1007/s00705-016-2886-8 10.1371/journal.pntd.0002636 10.1371/journal.pone.0012347 10.1146/annurev.genet.36.040202.111115 10.1093/nar/gkt1268 10.1093/nar/gkh340 10.1099/0022-1317-82-12-2945 10.1073/pnas.96.13.7352 10.1128/CMR.11.3.480 10.1016/0196-8858(86)90003-5 10.1073/pnas.241370698 10.1016/j.meegid.2017.01.022 10.1093/ve/vev023 10.1093/genetics/156.2.879 10.1186/1743-422X-7-227 |
| ContentType | Journal Article |
| Copyright | The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. 2017 The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. This work is published under http://creativecommons.org/licenses/by-nc/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License. |
| Copyright_xml | – notice: The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. 2017 – notice: The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. – notice: The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. This work is published under http://creativecommons.org/licenses/by-nc/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License. |
| DBID | TOX AAYXX CITATION CGR CUY CVF ECM EIF NPM 3V. 7QG 7QP 7QR 7SN 7SS 7TK 7TM 7TO 7U9 7X7 7XB 88A 88E 8AO 8FD 8FE 8FH 8FI 8FJ 8FK 8G5 ABUWG AEUYN AFKRA AZQEC BBNVY BENPR BHPHI C1K CCPQU DWQXO FR3 FYUFA GHDGH GNUQQ GUQSH H94 HCIFZ K9. LK8 M0S M1P M2O M7N M7P MBDVC P64 PHGZM PHGZT PJZUB PKEHL PPXIY PQEST PQGLB PQQKQ PQUKI PRINS Q9U RC3 7X8 5PM |
| DOI | 10.1093/molbev/msx263 |
| DatabaseName | Oxford Journals Open Access Collection CrossRef Medline MEDLINE MEDLINE (Ovid) MEDLINE MEDLINE PubMed ProQuest Central (Corporate) Animal Behavior Abstracts Calcium & Calcified Tissue Abstracts Chemoreception Abstracts Ecology Abstracts Entomology Abstracts (Full archive) Neurosciences Abstracts Nucleic Acids Abstracts Oncogenes and Growth Factors Abstracts Virology and AIDS Abstracts ProQuest Health & Medical Collection ProQuest Central (purchase pre-March 2016) Biology Database (Alumni Edition) Medical Database (Alumni Edition) ProQuest Pharma Collection Technology Research Database ProQuest SciTech Collection ProQuest Natural Science Collection Hospital Premium Collection Hospital Premium Collection (Alumni Edition) ProQuest Central (Alumni) (purchase pre-March 2016) Research Library (Alumni Edition) ProQuest Central (Alumni) ProQuest One Sustainability ProQuest Central UK/Ireland ProQuest Central Essentials Biological Science Collection AUTh Library subscriptions: ProQuest Central Natural Science Collection Environmental Sciences and Pollution Management ProQuest One Community College ProQuest Central Engineering Research Database Health Research Premium Collection Health Research Premium Collection (Alumni) ProQuest Central Student Research Library Prep AIDS and Cancer Research Abstracts SciTech Premium Collection ProQuest Health & Medical Complete (Alumni) ProQuest Biological Science Collection Health & Medical Collection (Alumni Edition) PML(ProQuest Medical Library) ProQuest Research Library Algology Mycology and Protozoology Abstracts (Microbiology C) Biological Science Database Research Library (Corporate) Biotechnology and BioEngineering Abstracts ProQuest Central Premium ProQuest One Academic ProQuest Health & Medical Research Collection ProQuest One Academic Middle East (New) ProQuest One Health & Nursing ProQuest One Academic Eastern Edition (DO NOT USE) ProQuest One Applied & Life Sciences ProQuest One Academic (retired) ProQuest One Academic UKI Edition ProQuest Central China ProQuest Central Basic Genetics Abstracts MEDLINE - Academic PubMed Central (Full Participant titles) |
| DatabaseTitle | CrossRef MEDLINE Medline Complete MEDLINE with Full Text PubMed MEDLINE (Ovid) Research Library Prep ProQuest Central Student Oncogenes and Growth Factors Abstracts ProQuest Central Essentials Nucleic Acids Abstracts SciTech Premium Collection ProQuest Central China Environmental Sciences and Pollution Management ProQuest One Applied & Life Sciences ProQuest One Sustainability Health Research Premium Collection Natural Science Collection Health & Medical Research Collection Biological Science Collection Chemoreception Abstracts ProQuest Central (New) ProQuest Medical Library (Alumni) Virology and AIDS Abstracts ProQuest Biological Science Collection ProQuest One Academic Eastern Edition ProQuest Hospital Collection Health Research Premium Collection (Alumni) Biological Science Database Ecology Abstracts Neurosciences Abstracts ProQuest Hospital Collection (Alumni) Biotechnology and BioEngineering Abstracts Entomology Abstracts ProQuest Health & Medical Complete ProQuest One Academic UKI Edition Engineering Research Database ProQuest One Academic Calcium & Calcified Tissue Abstracts ProQuest One Academic (New) Technology Research Database ProQuest One Academic Middle East (New) ProQuest Health & Medical Complete (Alumni) ProQuest Central (Alumni Edition) ProQuest One Community College ProQuest One Health & Nursing Research Library (Alumni Edition) ProQuest Natural Science Collection ProQuest Pharma Collection ProQuest Biology Journals (Alumni Edition) ProQuest Central ProQuest Health & Medical Research Collection Genetics Abstracts Health and Medicine Complete (Alumni Edition) ProQuest Central Korea Algology Mycology and Protozoology Abstracts (Microbiology C) AIDS and Cancer Research Abstracts ProQuest Research Library ProQuest Central Basic ProQuest SciTech Collection ProQuest Medical Library Animal Behavior Abstracts ProQuest Central (Alumni) MEDLINE - Academic |
| DatabaseTitleList | CrossRef MEDLINE - Academic Research Library Prep MEDLINE |
| Database_xml | – sequence: 1 dbid: NPM name: PubMed url: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed sourceTypes: Index Database – sequence: 2 dbid: TOX name: Oxford Journals Open Access Collection url: https://academic.oup.com/journals/ sourceTypes: Publisher – sequence: 3 dbid: BENPR name: ProQuest Central url: https://www.proquest.com/central sourceTypes: Aggregation Database |
| DeliveryMethod | fulltext_linktorsrc |
| Discipline | Biology |
| EISSN | 1537-1719 |
| EndPage | 251 |
| ExternalDocumentID | PMC5850291 29029186 10_1093_molbev_msx263 10.1093/molbev/msx263 |
| Genre | Research Support, Non-U.S. Gov't Journal Article |
| GrantInformation_xml | – fundername: Wellcome grantid: 089276/B/09/7; 098511/Z/12/Z funderid: 10.13039/100010269 – fundername: Wellcome Trust grantid: 089276/B/09/7 – fundername: Wellcome Trust grantid: 098511/Z/12/Z – fundername: Wellcome Trust – fundername: ; ; ; grantid: 089276/B/09/7 – fundername: ; ; ; grantid: 089276/B/09/7; 098511/Z/12/Z |
| GroupedDBID | --- -E4 -~X .2P .I3 .ZR 0R~ 18M 1TH 29M 2WC 4.4 48X 5VS 5WA 70D AAFWJ AAIJN AAIMJ AAJKP AAJQQ AAMDB AAMVS AAOGV AAPNW AAPQZ AAPXW AAUQX AAVAP AAVLN ABEUO ABIXL ABKDP ABLJU ABNKS ABPTD ABQLI ABXVV ABZBJ ACGFO ACGFS ACIPB ACIWK ACNCT ACPRK ACUFI ACUTO ACYTK ADBBV ADEYI ADEZT ADFTL ADGZP ADHKW ADHZD ADJQC ADOCK ADRIX ADRTK ADYVW ADZTZ ADZXQ AECKG AEGPL AEJOX AEKKA AEKSI AELWJ AEMDU AENEX AENZO AEPUE AETBJ AEWNT AFIYH AFOFC AFPKN AFRAH AFULF AFXEN AGINJ AGKEF AGSYK AHMBA AHXPO AIAGR AIJHB AJEUX AKHUL AKWXX ALMA_UNASSIGNED_HOLDINGS ALTZX ALUQC APIBT APWMN ARIXL AXUDD AYOIW AZVOD BAWUL BAYMD BCRHZ BEYMZ BHONS BQDIO BQUQU BSWAC BTQHN BTRTY BVRKM CDBKE CS3 CZ4 DAKXR DIK DILTD DU5 D~K E3Z EBS EE~ EJD EMOBN F5P F9B FHSFR FLIZI FOTVD GAUVT GJXCC GROUPED_DOAJ GX1 H13 H5~ HAR HH5 HW0 HZ~ IOX J21 KOP KQ8 KSI KSN M-Z M49 ML0 N9A NGC NLBLG NMDNZ NOYVH NU- O9- OAWHX ODMLO OJQWA OK1 OVD P2P PAFKI PEELM PQQKQ Q1. Q5Y RD5 RHF ROL ROX ROZ RPM RUSNO RW1 RXO TEORI TJP TJX TLC TN5 TOX TR2 VQA W8F WOQ X7H XSW YAYTL YKOAZ YXANX ZCA ZKX ~02 ~91 7X7 AAYXX ABEJV ABGNP ABUFD AMNDL BBNVY BENPR CITATION FYUFA CGR CUY CVF ECM EIF NPM 3V. 7QG 7QP 7QR 7SN 7SS 7TK 7TM 7TO 7U9 7XB 88A 88E 8AO 8FD 8FE 8FH 8FI 8FJ 8FK 8G5 ABUWG AEUYN AFKRA AZQEC BHPHI C1K CCPQU DWQXO FR3 GNUQQ GUQSH H94 HCIFZ K9. LK8 M1P M2O M7N M7P MBDVC P64 PHGZM PHGZT PJZUB PKEHL PPXIY PQEST PQGLB PQUKI PRINS Q9U RC3 7X8 5PM |
| ID | FETCH-LOGICAL-c542t-d27a2bf6c032d33423846867ebea39cb3aab61869ee52a08e745fa7e64cc280e3 |
| IEDL.DBID | M7P |
| ISICitedReferencesCount | 146 |
| ISICitedReferencesURI | http://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=Summon&SrcAuth=ProQuest&DestLinkType=CitingArticles&DestApp=WOS_CPL&KeyUT=000419548800020&url=https%3A%2F%2Fcvtisr.summon.serialssolutions.com%2F%23%21%2Fsearch%3Fho%3Df%26include.ft.matches%3Dt%26l%3Dnull%26q%3D |
| ISSN | 0737-4038 1537-1719 |
| IngestDate | Tue Nov 04 02:01:43 EST 2025 Thu Oct 02 11:12:24 EDT 2025 Mon Oct 06 17:54:05 EDT 2025 Mon Jul 21 06:04:57 EDT 2025 Sat Nov 29 05:53:02 EST 2025 Tue Nov 18 22:26:03 EST 2025 Wed Sep 11 04:48:06 EDT 2024 |
| IsDoiOpenAccess | true |
| IsOpenAccess | true |
| IsPeerReviewed | true |
| IsScholarly | true |
| Issue | 1 |
| Keywords | nonparametric recombination mosaic structure |
| Language | English |
| License | This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com http://creativecommons.org/licenses/by-nc/4.0 The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. |
| LinkModel | DirectLink |
| MergedId | FETCHMERGED-LOGICAL-c542t-d27a2bf6c032d33423846867ebea39cb3aab61869ee52a08e745fa7e64cc280e3 |
| Notes | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 14 content type line 23 Associate editor: Sergei Kosakovsky Pond |
| OpenAccessLink | https://dx.doi.org/10.1093/molbev/msx263 |
| PMID | 29029186 |
| PQID | 3170901760 |
| PQPubID | 36253 |
| PageCount | 5 |
| ParticipantIDs | pubmedcentral_primary_oai_pubmedcentral_nih_gov_5850291 proquest_miscellaneous_1951417956 proquest_journals_3170901760 pubmed_primary_29029186 crossref_citationtrail_10_1093_molbev_msx263 crossref_primary_10_1093_molbev_msx263 oup_primary_10_1093_molbev_msx263 |
| PublicationCentury | 2000 |
| PublicationDate | 2018-01-01 |
| PublicationDateYYYYMMDD | 2018-01-01 |
| PublicationDate_xml | – month: 01 year: 2018 text: 2018-01-01 day: 01 |
| PublicationDecade | 2010 |
| PublicationPlace | United States |
| PublicationPlace_xml | – name: United States – name: Oxford |
| PublicationTitle | Molecular biology and evolution |
| PublicationTitleAlternate | Mol Biol Evol |
| PublicationYear | 2018 |
| Publisher | Oxford University Press |
| Publisher_xml | – name: Oxford University Press |
| References | Hogan (2019121022373067600_msx263-B11) 1986; 7 Posada (2019121022373067600_msx263-B15) 2002; 54 Posada (2019121022373067600_msx263-B16) 2002; 36 Waman (2019121022373067600_msx263-B19) 2017; 49 Gubler (2019121022373067600_msx263-B9) 1998; 11 Boni (2019121022373067600_msx263-B2) 2010; 5 Brister (2019121022373067600_msx263-B4) 2014; 42 Uzcategui (2019121022373067600_msx263-B18) 2001; 82 Boni (2019121022373067600_msx263-B3) 2007; 176 Edgar (2019121022373067600_msx263-B6) 2004; 32 Martin (2019121022373067600_msx263-B13) 2011; 11 Wikramaratna (2019121022373067600_msx263-B21) 2010; 5 Ghedin (2019121022373067600_msx263-B8) 2005; 437 Posada (2019121022373067600_msx263-B14) 2001; 98 Schierup (2019121022373067600_msx263-B17) 2000; 156 Faye (2019121022373067600_msx263-B7) 2014; 8 Zhu (2019121022373067600_msx263-B23) 2016; 5 Worobey (2019121022373067600_msx263-B22) 1999; 96 Holmes (2019121022373067600_msx263-B12) 1999; 16 Dudas (2019121022373067600_msx263-B5) 2015; 2 Han (2019121022373067600_msx263-B10) 2010; 7 Aaskov (2019121022373067600_msx263-B1) 2007; 88 Waman (2019121022373067600_msx263-B20) 2016; 161 |
| References_xml | – volume: 5 start-page: e10434. issue: 5 year: 2010 ident: 2019121022373067600_msx263-B2 article-title: Guidelines for identifying homologous recombination events in influenza A virus publication-title: PLoS One doi: 10.1371/journal.pone.0010434 – volume: 176 start-page: 1035 issue: 2 year: 2007 ident: 2019121022373067600_msx263-B3 article-title: An exact nonparametric method for inferring mosaic structure in sequence triplets publication-title: Genetics doi: 10.1534/genetics.106.068874 – volume: 54 start-page: 396 issue: 3 year: 2002 ident: 2019121022373067600_msx263-B15 article-title: The effect of recombination on the accuracy of phylogeny estimation publication-title: J Mol Evol doi: 10.1007/s00239-001-0034-9 – volume: 437 start-page: 1162 issue: 7062 year: 2005 ident: 2019121022373067600_msx263-B8 article-title: Large-scale sequencing of human influenza reveals the dynamic nature of viral genome evolution publication-title: Nature doi: 10.1038/nature04239 – volume: 88 start-page: 3334 issue: 12 year: 2007 ident: 2019121022373067600_msx263-B1 article-title: Multiple recombinant dengue type 1 viruses in an isolate from a dengue patient publication-title: J Gen Virol doi: 10.1099/vir.0.83122-0 – volume: 5 start-page: e22 issue: 3 year: 2016 ident: 2019121022373067600_msx263-B23 article-title: Comparative genomic analysis of pre-epidemic and epidemic Zika virus strains for virological factors potentially associated with the rapidly expanding epidemic publication-title: Emerg Microb Infect – volume: 11 start-page: 943 issue: 6 year: 2011 ident: 2019121022373067600_msx263-B13 article-title: Analysing recombination in nucleotide sequences publication-title: Mol Ecol Resour doi: 10.1111/j.1755-0998.2011.03026.x – volume: 16 start-page: 405 issue: 3 year: 1999 ident: 2019121022373067600_msx263-B12 article-title: Phylogenetic evidence for recombination in dengue virus publication-title: Mol Biol Evol doi: 10.1093/oxfordjournals.molbev.a026121 – volume: 161 start-page: 2133 issue: 8 year: 2016 ident: 2019121022373067600_msx263-B20 article-title: Population genomics of dengue virus serotype 4: insights into genetic structure and evolution publication-title: Arch Virol doi: 10.1007/s00705-016-2886-8 – volume: 8 start-page: 36. issue: 1 year: 2014 ident: 2019121022373067600_msx263-B7 article-title: Molecular evolution of Zika virus during its emergence in the 20th century publication-title: PLoS Negl Trop Dis doi: 10.1371/journal.pntd.0002636 – volume: 5 start-page: e12347. issue: 8 year: 2010 ident: 2019121022373067600_msx263-B21 article-title: The effects of tertiary and quaternary infections on the epidemiology of dengue publication-title: PLoS One doi: 10.1371/journal.pone.0012347 – volume: 36 start-page: 75 issue: 1 year: 2002 ident: 2019121022373067600_msx263-B16 article-title: Recombination in evolutionary genomics publication-title: Annu Rev Genet doi: 10.1146/annurev.genet.36.040202.111115 – volume: 42 start-page: 660 issue: D1 year: 2014 ident: 2019121022373067600_msx263-B4 article-title: Virus variation resource – recent updates and future directions publication-title: Nucleic Acids Res. doi: 10.1093/nar/gkt1268 – volume: 32 start-page: 1792 issue: 5 year: 2004 ident: 2019121022373067600_msx263-B6 article-title: MUSCLE: multiple sequence alignment with high accuracy and high throughput publication-title: Nucleic Acids Res doi: 10.1093/nar/gkh340 – volume: 82 start-page: 2945 issue: 12 year: 2001 ident: 2019121022373067600_msx263-B18 article-title: Molecular epidemiology of dengue type 2 virus in Venezuela : evidence for in situ virus evolution and recombination publication-title: J Gen Virol doi: 10.1099/0022-1317-82-12-2945 – volume: 96 start-page: 7352 issue: 13 year: 1999 ident: 2019121022373067600_msx263-B22 article-title: Widespread intra-serotype recombination in natural populations of dengue virus publication-title: Proc Natl Acad Sci USA doi: 10.1073/pnas.96.13.7352 – volume: 11 start-page: 480 issue: 3 year: 1998 ident: 2019121022373067600_msx263-B9 article-title: Dengue and dengue hemorrhagic fever publication-title: Clin Microbiol Rev doi: 10.1128/CMR.11.3.480 – volume: 7 start-page: 2 issue: 1 year: 1986 ident: 2019121022373067600_msx263-B11 article-title: Large deviations for the maxima of some random fields publication-title: Adv Appl Math doi: 10.1016/0196-8858(86)90003-5 – volume: 98 start-page: 13757 issue: 24 year: 2001 ident: 2019121022373067600_msx263-B14 article-title: Evaluation of methods for detecting recombination from DNA sequences: computer simulations publication-title: Proc Natl Acad Sci USA doi: 10.1073/pnas.241370698 – volume: 49 start-page: 234 year: 2017 ident: 2019121022373067600_msx263-B19 article-title: Genetic diversity and evolution of dengue virus serotype 3: a comparative genomics study publication-title: Infect Genet Evol doi: 10.1016/j.meegid.2017.01.022 – volume: 2 start-page: vev023 issue: 1 year: 2015 ident: 2019121022373067600_msx263-B5 article-title: MERS-CoV recombination: implications about the reservoir and potential for adaptation publication-title: Virus Evol doi: 10.1093/ve/vev023 – volume: 156 start-page: 879 issue: 2 year: 2000 ident: 2019121022373067600_msx263-B17 article-title: Consequences of recombination on traditional phylogenetic analysis publication-title: Genetics doi: 10.1093/genetics/156.2.879 – volume: 7 start-page: 227. issue: 1 year: 2010 ident: 2019121022373067600_msx263-B10 article-title: No observed effect of homologous recombination on influenza C virus evolution publication-title: Virol J doi: 10.1186/1743-422X-7-227 |
| SSID | ssj0014466 |
| Score | 2.5870073 |
| Snippet | Abstract
Identifying recombinant sequences in an era of large genomic databases is challenging as it requires an efficient algorithm to identify candidate... Identifying recombinant sequences in an era of large genomic databases is challenging as it requires an efficient algorithm to identify candidate recombinants... |
| SourceID | pubmedcentral proquest pubmed crossref oup |
| SourceType | Open Access Repository Aggregation Database Index Database Enrichment Source Publisher |
| StartPage | 247 |
| SubjectTerms | Algorithms Biology Complexity Computation Datasets Gene Rearrangement - genetics Genomes Infectious diseases Methods Mosaicism Nucleotide sequence Phylogeny Probability Recombinants Recombination Recombination, Genetic - genetics Sequence Alignment - methods Sequence Analysis, DNA - methods Sequence Analysis, DNA - statistics & numerical data Software Statistical analysis Statistical methods Variables |
| Title | Improved Algorithmic Complexity for the 3SEQ Recombination Detection Algorithm |
| URI | https://www.ncbi.nlm.nih.gov/pubmed/29029186 https://www.proquest.com/docview/3170901760 https://www.proquest.com/docview/1951417956 https://pubmed.ncbi.nlm.nih.gov/PMC5850291 |
| Volume | 35 |
| WOSCitedRecordID | wos000419548800020&url=https%3A%2F%2Fcvtisr.summon.serialssolutions.com%2F%23%21%2Fsearch%3Fho%3Df%26include.ft.matches%3Dt%26l%3Dnull%26q%3D |
| hasFullText | 1 |
| inHoldings | 1 |
| isFullTextHit | |
| isPrint | |
| journalDatabaseRights | – providerCode: PRVASL databaseName: Oxford Journals Open Access Collection customDbUrl: eissn: 1537-1719 dateEnd: 99991231 omitProxy: false ssIdentifier: ssj0014466 issn: 0737-4038 databaseCode: TOX dateStart: 20020101 isFulltext: true titleUrlDefault: https://academic.oup.com/journals/ providerName: Oxford University Press – providerCode: PRVASL databaseName: Oxford Journals Open Access Collection customDbUrl: eissn: 1537-1719 dateEnd: 99991231 omitProxy: false ssIdentifier: ssj0014466 issn: 0737-4038 databaseCode: TOX dateStart: 19831201 isFulltext: true titleUrlDefault: https://academic.oup.com/journals/ providerName: Oxford University Press |
| link | http://cvtisr.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwpV3db9MwED-xDSRe-P4ojMpIiCeienYSO09oQCceoCswUN8i27mwSm06lmxi_z3nOM1WJOCBF0tRzonjs30_-y6_A3hhLJIdKNNIoyfVLlUZacNNxDErikxmRrS5Ab99UJOJns2yaXfgVndhles1sV2oi5XzZ-QjsnOcbJdK-euTH5HPGuW9q10KjS3Y8SwJog3dm_ZehLWvUklqBpe649ikTfxouVpYPB8t658ilRs2aeM_tytw8_eoyStm6OD2_37AHbjVAVC2H0bMXbiG1T24EVJSXtyHSThlwILtL75T9eZ4OXfMrxqeObO5YARyGYFGJr-MPzG_eV3S3rpVL3uHTRvYVV3WfQBfD8ZHb99HXc6FyCWxaKJCKCNsmTouRSE9PSABFJ0q0rWRmbPSGOsp9jPERBiuUcVJaRSmsXNCc5QPYbtaVfgYmNJobKySUnvcaK1ObIylTYxJ0OPOAbxa93ruOkJynxdjkQfHuMyDkvKgpAG87MVPAhPHnwSfkwr_JbO7VlLeTdo6v9QQPaK_TdPN-1BMhauzOt8jROqTtiXpAB6F8dC_SWRcZNQ3A1AbI6UX8FTem3eq-XFL6U2bNl_3yd-b9RRuEl7T4QRoF7ab0zN8BtfdeTOvT4ewpWaqLfUQdt6MJ9PPdPVRHA7bWUHl0eHsF5kfFxk |
| linkProvider | ProQuest |
| linkToHtml | http://cvtisr.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMw1V1Lb9QwEB6VAioX3o-FAkYCTkTr2knsHBCqaKtWXRYQpeot2IlDV9rNliYt7J_iNzITJ9suEnDqgbMdx4_PM-MZ-xuA58Y61ANFHGhHpNqFKgJtuAm4S_I8kYkRTW7A_YEaDvXBQfJhCX52b2HoWmUnExtBnU8z8pH3Uc9x1F0q5m-OvgWUNYqiq10KDQ-LXTf7jke26vXOBq7vCyG2NvfebgdtVoEgi0JRB7lQRtgizrgUuSQCPFTBOlY4GiOTzEpjLJHIJ85FwnDtVBgVRrk4zDKhuZPY7iW4HNJJiK4KivfzqEUXG1USh82lbjk9eSL7k-nYutP-pPohYrmgAxfe1Z0zb3-_pXlO7W3d-N8m7CZcbw1stu53xC1YcuVtuOpTbs7uwNB7UVzO1sdfsbv14WSUMZKKxAxazxga8QyNYiY_bX5kdDif2JH3mLINVzcX18qzb-_C5wsZzD1YLqelewBMaWdsqKJCk11srY5s6AobGRM5sqt78Kpb5TRrCdcp78c49YF_mXpQpB4UPXg5r37kmUb-VPEZQuZfdVY7UKStUKrSM0RgE_NiFCcUIzKlm55U6Rpa3JSULop7cN_jb_4nkXCR4Nz0QC0gc16BqMoXS8rRYUNZjodS-vbh37v1FFa2994N0sHOcPcRXEPbVHtv1yos18cn7jFcyU7rUXX8pNl3DL5cNG5_AdfBbsE |
| openUrl | ctx_ver=Z39.88-2004&ctx_enc=info%3Aofi%2Fenc%3AUTF-8&rfr_id=info%3Asid%2Fsummon.serialssolutions.com&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=Improved+Algorithmic+Complexity+for+the+3SEQ+Recombination+Detection+Algorithm&rft.jtitle=Molecular+biology+and+evolution&rft.au=Lam%2C+Ha+Minh&rft.au=Ratmann%2C+Oliver&rft.au=Boni%2C+Maciej+F&rft.date=2018-01-01&rft.eissn=1537-1719&rft.volume=35&rft.issue=1&rft.spage=247&rft_id=info:doi/10.1093%2Fmolbev%2Fmsx263&rft_id=info%3Apmid%2F29029186&rft.externalDocID=29029186 |
| thumbnail_l | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/lc.gif&issn=0737-4038&client=summon |
| thumbnail_m | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/mc.gif&issn=0737-4038&client=summon |
| thumbnail_s | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/sc.gif&issn=0737-4038&client=summon |