Using the longest run subsequence problem within homology-based scaffolding

Genome assembly is one of the most important problems in computational genomics. Here, we suggest addressing an issue that arises in homology-based scaffolding, that is, when linking and ordering contigs to obtain larger pseudo-chromosomes by means of a second incomplete assembly of a related specie...

Celý popis

Uloženo v:

Podrobná bibliografie
Vydáno v:	Algorithms for molecular biology Ročník 16; číslo 1; s. 1 - 11
Hlavní autoři:	Schrinner, Sven, Goel, Manish, Wulfert, Michael, Spohr, Philipp, Schneeberger, Korbinian, Klau, Gunnar W.
Médium:	Journal Article
Jazyk:	angličtina
Vydáno:	London BioMed Central 28.06.2021 Springer Nature B.V BMC
Témata:	Algorithms Alignment Assembly Bioinformatics Biomedical and Life Sciences Cellular and Medical Topics Chromosomes Computational Biology/Bioinformatics Computer applications Genomes Homology Life Sciences Linear programming Longest subsequence Mutation Physiological Scaffolding Selected papers from WABI 2020 Source code String algorithm String algorithm Alignment Longest subsequence Assembly
ISSN:	1748-7188, 1748-7188
On-line přístup:	Získat plný text
Tagy:	Přidat tag Žádné tagy, Buďte první, kdo vytvoří štítek k tomuto záznamu!

Abstract	Genome assembly is one of the most important problems in computational genomics. Here, we suggest addressing an issue that arises in homology-based scaffolding, that is, when linking and ordering contigs to obtain larger pseudo-chromosomes by means of a second incomplete assembly of a related species. The idea is to use alignments of binned regions in one contig to find the most homologous contig in the other assembly. We show that ordering the contigs of the other assembly can be expressed by a new string problem, the longest run subsequence problem (LRS). We show that LRS is NP-hard and present reduction rules and two algorithmic approaches that, together, are able to solve large instances of LRS to provable optimality. All data used in the experiments as well as our source code are freely available. We demonstrate its usefulness within an existing larger scaffolding approach by solving realistic instances resulting from partial Arabidopsis thaliana assemblies in short computation time.
AbstractList	Genome assembly is one of the most important problems in computational genomics. Here, we suggest addressing an issue that arises in homology-based scaffolding, that is, when linking and ordering contigs to obtain larger pseudo-chromosomes by means of a second incomplete assembly of a related species. The idea is to use alignments of binned regions in one contig to find the most homologous contig in the other assembly. We show that ordering the contigs of the other assembly can be expressed by a new string problem, the longest run subsequence problem (LRS). We show that LRS is NP-hard and present reduction rules and two algorithmic approaches that, together, are able to solve large instances of LRS to provable optimality. All data used in the experiments as well as our source code are freely available. We demonstrate its usefulness within an existing larger scaffolding approach by solving realistic instances resulting from partial Arabidopsis thaliana assemblies in short computation time.Genome assembly is one of the most important problems in computational genomics. Here, we suggest addressing an issue that arises in homology-based scaffolding, that is, when linking and ordering contigs to obtain larger pseudo-chromosomes by means of a second incomplete assembly of a related species. The idea is to use alignments of binned regions in one contig to find the most homologous contig in the other assembly. We show that ordering the contigs of the other assembly can be expressed by a new string problem, the longest run subsequence problem (LRS). We show that LRS is NP-hard and present reduction rules and two algorithmic approaches that, together, are able to solve large instances of LRS to provable optimality. All data used in the experiments as well as our source code are freely available. We demonstrate its usefulness within an existing larger scaffolding approach by solving realistic instances resulting from partial Arabidopsis thaliana assemblies in short computation time. Genome assembly is one of the most important problems in computational genomics. Here, we suggest addressing an issue that arises in homology-based scaffolding, that is, when linking and ordering contigs to obtain larger pseudo-chromosomes by means of a second incomplete assembly of a related species. The idea is to use alignments of binned regions in one contig to find the most homologous contig in the other assembly. We show that ordering the contigs of the other assembly can be expressed by a new string problem, the longest run subsequence problem (LRS). We show that LRS is NP-hard and present reduction rules and two algorithmic approaches that, together, are able to solve large instances of LRS to provable optimality. All data used in the experiments as well as our source code are freely available. We demonstrate its usefulness within an existing larger scaffolding approach by solving realistic instances resulting from partial Arabidopsis thaliana assemblies in short computation time. Genome assembly is one of the most important problems in computational genomics. Here, we suggest addressing an issue that arises in homology-based scaffolding, that is, when linking and ordering contigs to obtain larger pseudo-chromosomes by means of a second incomplete assembly of a related species. The idea is to use alignments of binned regions in one contig to find the most homologous contig in the other assembly. We show that ordering the contigs of the other assembly can be expressed by a new string problem, the longest run subsequence problem (LRS). We show that LRS is NP-hard and present reduction rules and two algorithmic approaches that, together, are able to solve large instances of LRS to provable optimality. All data used in the experiments as well as our source code are freely available. We demonstrate its usefulness within an existing larger scaffolding approach by solving realistic instances resulting from partial Arabidopsis thaliana assemblies in short computation time. Abstract Genome assembly is one of the most important problems in computational genomics. Here, we suggest addressing an issue that arises in homology-based scaffolding, that is, when linking and ordering contigs to obtain larger pseudo-chromosomes by means of a second incomplete assembly of a related species. The idea is to use alignments of binned regions in one contig to find the most homologous contig in the other assembly. We show that ordering the contigs of the other assembly can be expressed by a new string problem, the longest run subsequence problem (LRS). We show that LRS is NP-hard and present reduction rules and two algorithmic approaches that, together, are able to solve large instances of LRS to provable optimality. All data used in the experiments as well as our source code are freely available. We demonstrate its usefulness within an existing larger scaffolding approach by solving realistic instances resulting from partial Arabidopsis thaliana assemblies in short computation time.
ArticleNumber	11
Author	Klau, Gunnar W. Wulfert, Michael Spohr, Philipp Schrinner, Sven Schneeberger, Korbinian Goel, Manish
Author_xml	– sequence: 1 givenname: Sven surname: Schrinner fullname: Schrinner, Sven organization: Algorithmic Bioinformatics, Heinrich Heine University Düsseldorf – sequence: 2 givenname: Manish surname: Goel fullname: Goel, Manish organization: Max Planck Institute for Plant Breeding Research, Faculty of Biology, LMU Munich – sequence: 3 givenname: Michael surname: Wulfert fullname: Wulfert, Michael organization: Heinrich Heine University Düsseldorf – sequence: 4 givenname: Philipp surname: Spohr fullname: Spohr, Philipp organization: Algorithmic Bioinformatics, Heinrich Heine University Düsseldorf – sequence: 5 givenname: Korbinian surname: Schneeberger fullname: Schneeberger, Korbinian organization: Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University Düsseldorf, Max Planck Institute for Plant Breeding Research, Faculty of Biology, LMU Munich – sequence: 6 givenname: Gunnar W. orcidid: 0000-0002-6340-0090 surname: Klau fullname: Klau, Gunnar W. email: gunnar.klau@hhu.de organization: Algorithmic Bioinformatics, Heinrich Heine University Düsseldorf, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University Düsseldorf
BookMark	eNp9kktv1TAQhS1URB_wB1hFYsMmYDt-bpBQxaOiEhu6thxnkusrx77YCaj_Ht-mAtpFVx7Z53wzmuNzdBJTBIReE_yOECXeF9JhwltMSYsx0aRVz9AZkUy1kih18l99is5L2WPMeIe7F-i0Y0TVSpyhbzfFx6lZdtCEFCcoS5PX2JS1L_BzheigOeTUB5ib337Z-djs0pxCmm7b3hYYmuLsOKYwVMpL9Hy0ocCr-_MC3Xz-9OPya3v9_cvV5cfr1nEil9ZSpyVxdJC9U87KkWoMDnrsiFZ6GNhAsVNCWC30OGrH8OgEp5ZpThUw2V2gq407JLs3h-xnm29Nst7cXaQ8GZsX7wIYJnDXO96NEjTDnGkNPVg8CsEcc8OR9WFjHdZ-hsFBXLIND6APX6LfmSn9MooyTGVXAW_vATnVhZXFzL44CMFGSGsxlDPBteKaV-mbR9J9WnOsq6oqTqVQnLGqopvK5VRKhvHvMASbY-5my93U3M1d7kZVk3pkcn6xi0_HoX142tpt1lL71B-Q_031hOsPIIbDeQ
CitedBy_id	crossref_primary_10_1007_s00236_024_00459_7 crossref_primary_10_1016_j_ic_2025_105313
Cites_doi	10.1186/s13059-019-1911-0 10.1101/gr.214874.116 10.1093/bioinformatics/btaa253 10.1186/s13059-019-1829-6 10.1186/s13059-014-0573-1 10.1287/opre.32.6.1195 10.1186/s13059-017-1213-3 10.1038/35048692 10.1038/nbt.2727 10.1093/bioinformatics/bts480 10.1371/journal.pcbi.1005944 10.1101/gr.213652.116
ContentType	Journal Article
Copyright	The Author(s) 2021 2021. This work is licensed under http://creativecommons.org/licenses/by/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(s) 2021 – notice: 2021. This work is licensed under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.
DBID	C6C AAYXX CITATION 3V. 7QO 7QP 7QR 7TK 7X7 7XB 8FD 8FE 8FG 8FH 8FI 8FJ 8FK ABJCF ABUWG AEUYN AFKRA ARAPS AZQEC BBNVY BENPR BGLVJ BHPHI CCPQU DWQXO FR3 FYUFA GHDGH GNUQQ HCIFZ K9. L6V LK8 M0S M7P M7S P5Z P62 P64 PHGZM PHGZT PIMPY PJZUB PKEHL PPXIY PQEST PQGLB PQQKQ PQUKI PRINS PTHSS 7X8 5PM DOA
DOI	10.1186/s13015-021-00191-8
DatabaseName	Springer Nature OA Free Journals CrossRef ProQuest Central (Corporate) Biotechnology Research Abstracts Calcium & Calcified Tissue Abstracts Chemoreception Abstracts Neurosciences Abstracts Health & Medical Collection ProQuest Central (purchase pre-March 2016) Technology Research Database ProQuest SciTech Collection ProQuest Technology Collection ProQuest Natural Science Journals Hospital Premium Collection Hospital Premium Collection (Alumni Edition) ProQuest Central (Alumni) (purchase pre-March 2016) Materials Science & Engineering Collection ProQuest Central (Alumni) ProQuest One Sustainability (subscription) ProQuest Central UK/Ireland Advanced Technologies & Computer Science Collection ProQuest Central Essentials Biological Science Database (Proquest) ProQuest Central Technology collection Natural Science Collection ProQuest One Community College ProQuest Central Engineering Research Database Health Research Premium Collection Health Research Premium Collection (Alumni) ProQuest Central Student SciTech Premium Collection ProQuest Health & Medical Complete (Alumni) ProQuest Engineering Collection Biological Sciences ProQuest Health & Medical Collection Biological Science Database Engineering Database Advanced Technologies & Aerospace Database ProQuest Advanced Technologies & Aerospace Collection Biotechnology and BioEngineering Abstracts ProQuest Central Premium ProQuest One Academic Publicly Available Content Database ProQuest Health & Medical Research Collection ProQuest One Academic Middle East (New) 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 Engineering Collection MEDLINE - Academic PubMed Central (Full Participant titles) DOAJ Directory of Open Access Journals
DatabaseTitle	CrossRef Publicly Available Content Database ProQuest Central Student ProQuest Advanced Technologies & Aerospace Collection ProQuest Central Essentials SciTech Premium Collection ProQuest Central China ProQuest One Applied & Life Sciences ProQuest One Sustainability Health Research Premium Collection Natural Science Collection Biological Science Collection Chemoreception Abstracts ProQuest Central (New) Engineering Collection Advanced Technologies & Aerospace Collection Engineering Database ProQuest Biological Science Collection ProQuest One Academic Eastern Edition ProQuest Hospital Collection ProQuest Technology Collection Health Research Premium Collection (Alumni) Biological Science Database Neurosciences Abstracts ProQuest Hospital Collection (Alumni) Biotechnology and BioEngineering 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 Collection 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 ProQuest Natural Science Collection ProQuest Central ProQuest Health & Medical Research Collection ProQuest Engineering Collection Biotechnology Research Abstracts Health and Medicine Complete (Alumni Edition) ProQuest Central Korea ProQuest SciTech Collection Advanced Technologies & Aerospace Database Materials Science & Engineering Collection ProQuest Central (Alumni) MEDLINE - Academic
DatabaseTitleList	MEDLINE - Academic CrossRef Publicly Available Content Database
Database_xml	– sequence: 1 dbid: DOA name: DOAJ Directory of Open Access Journals url: https://www.doaj.org/ sourceTypes: Open Website – sequence: 2 dbid: PIMPY name: Publicly Available Content Database url: http://search.proquest.com/publiccontent sourceTypes: Aggregation Database
DeliveryMethod	fulltext_linktorsrc
Discipline	Biology
EISSN	1748-7188
EndPage	11
ExternalDocumentID	oai_doaj_org_article_4603bc53f7e9405499ebea0f664c4cd7 PMC8240273 10_1186_s13015_021_00191_8
GrantInformation_xml	– fundername: Heinrich-Heine-Universität Düsseldorf (3102) – fundername: Deutsche Forschungsgemeinschaft grantid: 390686111 funderid: http://dx.doi.org/10.13039/501100001659 – fundername: ; – fundername: ; grantid: 390686111
GroupedDBID	0R~ 23M 2WC 53G 5GY 5VS 6J9 7X7 8FE 8FG 8FH 8FI 8FJ AAFWJ AAJSJ AASML ABDBF ABJCF ABUWG ACGFO ACGFS ACIHN ACIWK ACPRK ACUHS ADBBV ADMLS ADRAZ ADUKV AEAQA AENEX AEUYN AFKRA AFPKN AFRAH AHBYD AHMBA AHYZX ALMA_UNASSIGNED_HOLDINGS AMKLP AMTXH AOIJS ARAPS BAPOH BAWUL BBNVY BCNDV BENPR BFQNJ BGLVJ BHPHI BMC BPHCQ BVXVI C6C CCPQU CS3 DIK E3Z EBD EBLON EBS ESX F5P FYUFA GROUPED_DOAJ GX1 HCIFZ HMCUK HYE IAO IGS IHR ITC KQ8 L6V LK8 M48 M7P M7S M~E O5R O5S OK1 OVT P2P P62 PGMZT PHGZM PHGZT PIMPY PQGLB PQQKQ PROAC PTHSS PUEGO RBZ RNS ROL RPM RSV SBL SOJ TR2 TUS UKHRP WOQ WOW ~8M AAYXX AFFHD CITATION 3V. 7QO 7QP 7QR 7TK 7XB 8FD 8FK AZQEC DWQXO FR3 GNUQQ K9. P64 PJZUB PKEHL PPXIY PQEST PQUKI PRINS 7X8 5PM
ID	FETCH-LOGICAL-c517t-a2c971c2d7bc8ca7f290eceb0c1989dd4d20c866a969ff9c40fc652a49528e473
IEDL.DBID	M7P
ISICitedReferencesCount	4
ISICitedReferencesURI	http://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=Summon&SrcAuth=ProQuest&DestLinkType=CitingArticles&DestApp=WOS_CPL&KeyUT=000669596900002&url=https%3A%2F%2Fcvtisr.summon.serialssolutions.com%2F%23%21%2Fsearch%3Fho%3Df%26include.ft.matches%3Dt%26l%3Dnull%26q%3D
ISSN	1748-7188
IngestDate	Tue Oct 14 18:43:38 EDT 2025 Tue Nov 04 01:37:59 EST 2025 Thu Oct 02 10:12:45 EDT 2025 Sat Nov 29 14:28:03 EST 2025 Tue Nov 18 21:18:21 EST 2025 Sat Nov 29 05:10:44 EST 2025 Sat Sep 06 07:29:42 EDT 2025
IsDoiOpenAccess	true
IsOpenAccess	true
IsPeerReviewed	true
IsScholarly	true
Issue	1
Keywords	String algorithm Alignment Longest subsequence Assembly
Language	English
License	Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
LinkModel	DirectLink
MergedId	FETCHMERGED-LOGICAL-c517t-a2c971c2d7bc8ca7f290eceb0c1989dd4d20c866a969ff9c40fc652a49528e473
Notes	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 14 content type line 23
ORCID	0000-0002-6340-0090
OpenAccessLink	https://www.proquest.com/docview/2552768544?pq-origsite=%requestingapplication%
PMID	34183036
PQID	2552768544
PQPubID	55040
PageCount	11
ParticipantIDs	doaj_primary_oai_doaj_org_article_4603bc53f7e9405499ebea0f664c4cd7 pubmedcentral_primary_oai_pubmedcentral_nih_gov_8240273 proquest_miscellaneous_2546598595 proquest_journals_2552768544 crossref_primary_10_1186_s13015_021_00191_8 crossref_citationtrail_10_1186_s13015_021_00191_8 springer_journals_10_1186_s13015_021_00191_8
PublicationCentury	2000
PublicationDate	2021-06-28
PublicationDateYYYYMMDD	2021-06-28
PublicationDate_xml	– month: 06 year: 2021 text: 2021-06-28 day: 28
PublicationDecade	2020
PublicationPlace	London
PublicationPlace_xml	– name: London
PublicationTitle	Algorithms for molecular biology
PublicationTitleAbbrev	Algorithms Mol Biol
PublicationYear	2021
Publisher	BioMed Central Springer Nature B.V BMC
Publisher_xml	– name: BioMed Central – name: Springer Nature B.V – name: BMC
References	The Arabidopsis Genome Initiative (191_CR11) 2000; 408 H Tang (191_CR3) 2015; 16 M Alonge (191_CR1) 2019; 20 NI Weisenfeld (191_CR4) 2017; 27 M Grötschel (191_CR9) 1984; 32 H Alhakami (191_CR8) 2017; 18 J Köster (191_CR10) 2012; 28 L Coombe (191_CR2) 2020 W-B Jiao (191_CR6) 2017; 27 191_CR13 M Goel (191_CR7) 2019; 20 JN Burton (191_CR5) 2013; 31 G Marcais (191_CR12) 2018; 14
References_xml	– volume: 20 start-page: 277 issue: 1 year: 2019 ident: 191_CR7 publication-title: Genome Biol doi: 10.1186/s13059-019-1911-0 – volume: 27 start-page: 757 issue: 5 year: 2017 ident: 191_CR4 publication-title: Genome Res doi: 10.1101/gr.214874.116 – year: 2020 ident: 191_CR2 publication-title: Bioinformatics. doi: 10.1093/bioinformatics/btaa253 – volume: 20 start-page: 224 issue: 1 year: 2019 ident: 191_CR1 publication-title: Genome Biol doi: 10.1186/s13059-019-1829-6 – volume: 16 start-page: 3 issue: 1 year: 2015 ident: 191_CR3 publication-title: Genome Biol doi: 10.1186/s13059-014-0573-1 – volume: 32 start-page: 1195 year: 1984 ident: 191_CR9 publication-title: Operations Res doi: 10.1287/opre.32.6.1195 – ident: 191_CR13 – volume: 18 start-page: 93 issue: 1 year: 2017 ident: 191_CR8 publication-title: Genome Biol doi: 10.1186/s13059-017-1213-3 – volume: 408 start-page: 796 issue: 6814 year: 2000 ident: 191_CR11 publication-title: Nature doi: 10.1038/35048692 – volume: 31 start-page: 1119 issue: 12 year: 2013 ident: 191_CR5 publication-title: Nat Biotechnol doi: 10.1038/nbt.2727 – volume: 28 start-page: 2520 issue: 19 year: 2012 ident: 191_CR10 publication-title: Bioinformatics doi: 10.1093/bioinformatics/bts480 – volume: 14 start-page: 1 issue: 1 year: 2018 ident: 191_CR12 publication-title: PLOS Comput Biol doi: 10.1371/journal.pcbi.1005944 – volume: 27 start-page: 778 issue: 5 year: 2017 ident: 191_CR6 publication-title: Genome Res doi: 10.1101/gr.213652.116
SSID	ssj0045303
Score	2.2740846
Snippet	Genome assembly is one of the most important problems in computational genomics. Here, we suggest addressing an issue that arises in homology-based... Abstract Genome assembly is one of the most important problems in computational genomics. Here, we suggest addressing an issue that arises in homology-based...
SourceID	doaj pubmedcentral proquest crossref springer
SourceType	Open Website Open Access Repository Aggregation Database Enrichment Source Index Database Publisher
StartPage	1
SubjectTerms	Algorithms Alignment Assembly Bioinformatics Biomedical and Life Sciences Cellular and Medical Topics Chromosomes Computational Biology/Bioinformatics Computer applications Genomes Homology Life Sciences Linear programming Longest subsequence Mutation Physiological Scaffolding Selected papers from WABI 2020 Source code String algorithm
SummonAdditionalLinks	– databaseName: DOAJ Directory of Open Access Journals dbid: DOA link: http://cvtisr.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwrV3Ni9UwEB9kWcGLrF9Yd10ieNOwbZrm46jLLoKweFDYW0inCftg7ZPX9wT_eydp-7QL6sVj24Qkk8l8dCa_AXgdQoOkOJCTrkIuQ0RufSoJaIy3pYpo65iLTeirK3N9bT_9Vuor5YSN8MAj4c6kKusWmzrqYMm4IAOdhvVlVEqixC7fIyerZ3amRhksG5LM8xUZo84GktRVuolMrjPZNBU3CzWU0foXJubdBMk7UdKsfC6P4OFkNbJ342wfwb3QP4b7Yx3JH0_gYw78M7Ll2O26TxEjttn1bCChMGVKs6lwDEv_XVc9u1l_zX150mIdG9DHOMahnsKXy4vP5x_4VCWBY1PpLfcCra5QdLpFg15HYcuAoS0xpUN1nexEiUYpb5WN0aIsI6pGePKMhAlS18_goF_34Tmw6A15Y502XWVlKxt61K2JrUp2oBKigGommsMJQjxVsrh12ZUwyo2EdkRolwntTAFv9n2-jQAaf239Pu3FvmUCv84viCXcxBLuXyxRwMm8k246kYMTCWpOmUbKAl7tP9NZSgES34f1LrWRqrEJ8a0AveCAxYSWX_rVTUblNilOpesC3s688mvwPy_4xf9Y8DE8EJm3FRfmBA62m114CYf4fbsaNqf5ZPwESoYRtw priority: 102 providerName: Directory of Open Access Journals – databaseName: SpringerLINK Contemporary 1997-Present dbid: RSV link: http://cvtisr.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwnR3batVAcKitgi9tvWFqLSv4povJZrOXR5WWQqGUeqFvy2ayaw_URE7OEfx7dzfJkRQV9DHZGbKZzDUzOwPw0rkKg-FAGmwVUu48Um3jSEClrM6FR136NGxCnp-rqyt9MR4K66dq9yklmTR1Emsl3vRB2xbxNHEIf4NfUlB1B3aCuVNRHC8_fJ70L6-CVp6Ox_wWb2aCUqf-mXt5uzjyVoY0GZ6Tvf_b8j7sjo4meTtwxgPYcu1DuDeMnvzxCM5SrQAJ7h-56dqYZCLLdUv6oEfG4moyzpoh8VftoiXX3deES6Pha0iP1vshdfUYPp0cf3x_SsfBChSrQq6oZahlgayRNSq00jOdO3R1jrGCqml4w3JUQlgttPcaee5RVMyGYIopx2X5BLbbrnVPgXirQgDXSNUUmte8CpeyVr4W0XUUjGVQTLQ2OHYdj8MvbkyKPpQwA5FMIJJJRDIqg1cbnG9Dz42_Qr-Ln3ADGftlpxvd8osZxc9wkZc1VqWXTgcXNYR5gXlt7oXgyLGRGRxODGBGIe4Ni93phKo4z-DFZjmIX8yp2NZ16wjDRaVjk7gM5IxxZhuar7SL69TIW8XUliwzeD2xz6-H__mFD_4N_BncZ4kDBWXqELZXy7V7Dnfx-2rRL4-S6PwEN7sVkw priority: 102 providerName: Springer Nature
Title	Using the longest run subsequence problem within homology-based scaffolding
URI	https://link.springer.com/article/10.1186/s13015-021-00191-8 https://www.proquest.com/docview/2552768544 https://www.proquest.com/docview/2546598595 https://pubmed.ncbi.nlm.nih.gov/PMC8240273 https://doaj.org/article/4603bc53f7e9405499ebea0f664c4cd7
Volume	16
WOSCitedRecordID	wos000669596900002&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: PRVADU databaseName: BioMedCentral Open Access database customDbUrl: eissn: 1748-7188 dateEnd: 99991231 omitProxy: false ssIdentifier: ssj0045303 issn: 1748-7188 databaseCode: RBZ dateStart: 20060101 isFulltext: true titleUrlDefault: https://www.biomedcentral.com/search/ providerName: BioMedCentral – providerCode: PRVAON databaseName: DOAJ Directory of Open Access Journals customDbUrl: eissn: 1748-7188 dateEnd: 99991231 omitProxy: false ssIdentifier: ssj0045303 issn: 1748-7188 databaseCode: DOA dateStart: 20060101 isFulltext: true titleUrlDefault: https://www.doaj.org/ providerName: Directory of Open Access Journals – providerCode: PRVHPJ databaseName: ROAD: Directory of Open Access Scholarly Resources customDbUrl: eissn: 1748-7188 dateEnd: 99991231 omitProxy: false ssIdentifier: ssj0045303 issn: 1748-7188 databaseCode: M~E dateStart: 20060101 isFulltext: true titleUrlDefault: https://road.issn.org providerName: ISSN International Centre – providerCode: PRVPQU databaseName: Advanced Technologies & Aerospace Database customDbUrl: eissn: 1748-7188 dateEnd: 99991231 omitProxy: false ssIdentifier: ssj0045303 issn: 1748-7188 databaseCode: P5Z dateStart: 20090101 isFulltext: true titleUrlDefault: https://search.proquest.com/hightechjournals providerName: ProQuest – providerCode: PRVPQU databaseName: Biological Science Database customDbUrl: eissn: 1748-7188 dateEnd: 99991231 omitProxy: false ssIdentifier: ssj0045303 issn: 1748-7188 databaseCode: M7P dateStart: 20090101 isFulltext: true titleUrlDefault: http://search.proquest.com/biologicalscijournals providerName: ProQuest – providerCode: PRVPQU databaseName: Engineering Database customDbUrl: eissn: 1748-7188 dateEnd: 99991231 omitProxy: false ssIdentifier: ssj0045303 issn: 1748-7188 databaseCode: M7S dateStart: 20090101 isFulltext: true titleUrlDefault: http://search.proquest.com providerName: ProQuest – providerCode: PRVPQU databaseName: Health & Medical Collection customDbUrl: eissn: 1748-7188 dateEnd: 99991231 omitProxy: false ssIdentifier: ssj0045303 issn: 1748-7188 databaseCode: 7X7 dateStart: 20090101 isFulltext: true titleUrlDefault: https://search.proquest.com/healthcomplete providerName: ProQuest – providerCode: PRVPQU databaseName: ProQuest Central customDbUrl: eissn: 1748-7188 dateEnd: 99991231 omitProxy: false ssIdentifier: ssj0045303 issn: 1748-7188 databaseCode: BENPR dateStart: 20090101 isFulltext: true titleUrlDefault: https://www.proquest.com/central providerName: ProQuest – providerCode: PRVPQU databaseName: Publicly Available Content Database customDbUrl: eissn: 1748-7188 dateEnd: 99991231 omitProxy: false ssIdentifier: ssj0045303 issn: 1748-7188 databaseCode: PIMPY dateStart: 20090101 isFulltext: true titleUrlDefault: http://search.proquest.com/publiccontent providerName: ProQuest – providerCode: PRVAVX databaseName: SpringerLINK Contemporary 1997-Present customDbUrl: eissn: 1748-7188 dateEnd: 99991231 omitProxy: false ssIdentifier: ssj0045303 issn: 1748-7188 databaseCode: RSV dateStart: 20060101 isFulltext: true titleUrlDefault: https://link.springer.com/search?facet-content-type=%22Journal%22 providerName: Springer Nature
link	http://cvtisr.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwpR1da9Uw9OA2BV_8FqvzEsE3DWvTNB9P4mRDES9lU7n6UtrTxF2Y7by9V_Dfm6TtHR24F18CaRKa9pyc75wD8NKYDB3jQOp4FVJuLFJd-pKASpU6FhZ1akOxCTmfq8VC54PBrRvCKkeaGAh13aK3kR8wnypMqIzzNxe_qK8a5b2rQwmNHdjzWRLSELqXj5SYZ44-jxdllDjoHL1O_H1kp0A7ySahasKMQs7-iaB5NUzyiq80sKDju_-7-XtwZxA-ydseW-7DDdM8gFt9Oco_D-FjiB8gTiQk523jHU9ktWlI52jLEHBNhvozxJtvlw05a3-GtdQzw5p0WFrbu7MewZfjo8_v3tOh2ALFLJFrWjLUMkFWywoVltIyHRs0VYw-qqquec1iVEKUWmhrNfLYoshY6RQspgyX6WPYbdrGPAFiS-WUulqqOtG84pnrykrZSnhxUjAWQTL-9QKHTOS-IMZ5ETQSJYoeUoWDVBEgVagIXm3XXPR5OK6dfeiBuZ3pc2iHB-3qRzEcyYKLOK0wS6002omtTvVzCF3GVgiOHGsZwf4IzGI42F1xCckIXmyH3ZH0fpayMe3Gz-Ei0z5xXARygkKTDU1HmuVZSO6tvLtLphG8HpHt8uX__uCn1-_1GdxmAe0FZWofdterjXkON_H3etmtZrAjFzK0agZ7h0fz_GQWbBOzcJxCe-raPPvuxvMPn_Jvrndy-vUvnlso2g
linkProvider	ProQuest
linkToHtml	http://cvtisr.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMw1V1Lb9QwEB6VAoILb9RAASPBCaImjuPHASFeVastqx6K1JtJJjZdqU3KZhfUP8VvxHaSrVKJ3nrgmMROnPjzPDLj-QBeGZOjUxwYO12FMTMWY1V4SkApC5VwiyqzgWxCTKfy8FDtr8GfYS-MT6scZGIQ1FWD_h_5FvWlwrjMGXt_-jP2rFE-ujpQaHSwmJiz385la9_tfnbz-5rS7S8Hn3binlUgxjwVi7igqESKtBIlSiyEpSoxaMoEffpQVbGKJig5LxRX1ipkiUWe08J5ElQaJjJ332tw3ZkRVIZUwf1B8rPc6YNhY47kW63TD6nf_-wcdmdJpbEcKb_AETAybC-mZV6IzQaVt333f_tY9-BOb1yTD91quA9rpn4ANzu6zbOHMAn5EcSZvOS4qX1gjcyXNWmd7OwTyknPr0P87-lZTY6ak9A39sq-Ii0W1nbhukfw7Ure5DGs101tNoDYQjqntRKyShUrWe4ORSltyb25zCmNIB1mWWNfad0Tfhzr4HFJrjtkaIcMHZChZQRvVn1Ouzojl7b-6MGzaulrhIcTzfyH7kWOZjzJSswzK4xyZrlzbd2CLRLLOUOGlYhgcwCP7gVXq8-RE8HL1WUncnwcqahNs_RtGM-VL4wXgRhBdjSg8ZV6dhSKl0sfzhNZBG8HcJ8__N8v_OTysb6AWzsHX_f03u508hRu07DkeEzlJqwv5kvzDG7gr8WsnT8PC5bA96sG_V8TaX3E
linkToPdf	http://cvtisr.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwpR3ZbtQwcAQFqr5wVw0UMBJvEDVxHB-PXCtQ0aoSh_pmORO7Xakk1Wa3En9f20kWUgES4jHxWHEmc2YugBfWlugVB6ZeV2HKrMNUmTASUEqjMu5QFS4OmxDzuTw-Vke_VPHHbPcxJNnXNIQuTc3q4Lx2PYtLftB5yZuHymLvCnsbJU_ldbjBwtCg4K9__jbKYlZ6CT2Wyvx230Qdxa79E1PzaqLklWhpVEKzO_9__LtwezBAyeueYu7BNdvch1v9SMofD-Aw5hAQbxaSs7YJwSeyXDek8_JlSLomwwwaEn7hLhpy2n6Pe9OgEGvSoXGuD2k9hK-z91_efkiHgQsplrlYpYaiEjnSWlQo0QhHVWbRVhmGzKq6ZjXNUHJuFFfOKWSZQ15S450sKi0TxS5sNW1j94A4I71jVwtZ54pVrPSXopKu4sGk5JQmkI941zh0Iw9DMc509Eok1z2StEeSjkjSMoGXmz3nfS-Ov0K_CZ9zAxn6aMcb7fJED2ypGc-KCsvCCau86erdP0_UJnOcM2RYiwT2R2LQA3N3moaudVyWjCXwfLPs2TLEWkxj23WAYbxUoXlcAmJCRJMDTVeaxWls8C1DyEsUCbwaSennw__8wo_-DfwZbB-9m-lPH-eHj2GHRmLkKZX7sLVaru0TuIkXq0W3fBo56hJMNiFb
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=Using+the+longest+run+subsequence+problem+within+homology-based+scaffolding&rft.jtitle=Algorithms+for+molecular+biology&rft.au=Schrinner%2C+Sven&rft.au=Goel%2C+Manish&rft.au=Wulfert%2C+Michael&rft.au=Spohr%2C+Philipp&rft.date=2021-06-28&rft.issn=1748-7188&rft.eissn=1748-7188&rft.volume=16&rft.issue=1&rft.spage=11&rft_id=info:doi/10.1186%2Fs13015-021-00191-8&rft.externalDBID=NO_FULL_TEXT
thumbnail_l	http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/lc.gif&issn=1748-7188&client=summon
thumbnail_m	http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/mc.gif&issn=1748-7188&client=summon
thumbnail_s	http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/sc.gif&issn=1748-7188&client=summon