Algorithms for optimizing cross-overs in DNA shuffling
Background DNA shuffling generates combinatorial libraries of chimeric genes by stochastically recombining parent genes. The resulting libraries are subjected to large-scale genetic selection or screening to identify those chimeras with favorable properties (e.g., enhanced stability or enzymatic act...
Uloženo v:
| Vydáno v: | BMC bioinformatics Ročník 13; číslo Suppl 3; s. S3 |
|---|---|
| Hlavní autoři: | , , |
| Médium: | Journal Article |
| Jazyk: | angličtina |
| Vydáno: |
London
BioMed Central
21.03.2012
Springer Nature B.V |
| Témata: | |
| ISSN: | 1471-2105, 1471-2105 |
| On-line přístup: | Získat plný text |
| Tagy: |
Přidat tag
Žádné tagy, Buďte první, kdo vytvoří štítek k tomuto záznamu!
|
| Abstract | Background
DNA shuffling generates combinatorial libraries of chimeric genes by stochastically recombining parent genes. The resulting libraries are subjected to large-scale genetic selection or screening to identify those chimeras with favorable properties (e.g., enhanced stability or enzymatic activity). While DNA shuffling has been applied quite successfully, it is limited by its homology-dependent, stochastic nature. Consequently, it is used only with parents of sufficient overall sequence identity, and provides no control over the resulting chimeric library.
Results
This paper presents efficient methods to extend the scope of DNA shuffling to handle significantly more diverse parents and to generate more predictable, optimized libraries. Our C
ODNS
(cross-over optimization for DNA shuffling) approach employs polynomial-time dynamic programming algorithms to select codons for the parental amino acids, allowing for zero or a fixed number of conservative substitutions. We first present efficient algorithms to optimize the local sequence identity or the nearest-neighbor approximation of the change in free energy upon annealing, objectives that were previously optimized by computationally-expensive integer programming methods. We then present efficient algorithms for more powerful objectives that seek to localize and enhance the frequency of recombination by producing "runs" of common nucleotides either overall or according to the sequence diversity of the resulting chimeras. We demonstrate the effectiveness of C
ODNS
in choosing codons and allocating substitutions to promote recombination between parents targeted in earlier studies: two GAR transformylases (41% amino acid sequence identity), two very distantly related DNA polymerases, Pol X and
β
(15%), and beta-lactamases of varying identity (26-47%).
Conclusions
Our methods provide the protein engineer with a new approach to DNA shuffling that supports substantially more diverse parents, is more deterministic, and generates more predictable and more diverse chimeric libraries. |
|---|---|
| AbstractList | Background: DNA shuffling generates combinatorial libraries of chimeric genes by stochastically recombining parent genes. The resulting libraries are subjected to large-scale genetic selection or screening to identify those chimeras with favorable properties (e.g., enhanced stability or enzymatic activity). While DNA shuffling has been applied quite successfully, it is limited by its homology-dependent, stochastic nature. Consequently, it is used only with parents of sufficient overall sequence identity, and provides no control over the resulting chimeric library. Results: This paper presents efficient methods to extend the scope of DNA shuffling to handle significantly more diverse parents and to generate more predictable, optimized libraries. Our C ODNS (cross-over optimization for DNA shuffling) approach employs polynomial-time dynamic programming algorithms to select codons for the parental amino acids, allowing for zero or a fixed number of conservative substitutions. We first present efficient algorithms to optimize the local sequence identity or the nearest-neighbor approximation of the change in free energy upon annealing, objectives that were previously optimized by computationally-expensive integer programming methods. We then present efficient algorithms for more powerful objectives that seek to localize and enhance the frequency of recombination by producing "runs" of common nucleotides either overall or according to the sequence diversity of the resulting chimeras. We demonstrate the effectiveness of C ODNS in choosing codons and allocating substitutions to promote recombination between parents targeted in earlier studies: two GAR transformylases (41% amino acid sequence identity), two very distantly related DNA polymerases, Pol X and [beta] (15%), and beta-lactamases of varying identity (26-47%). Conclusions: Our methods provide the protein engineer with a new approach to DNA shuffling that supports substantially more diverse parents, is more deterministic, and generates more predictable and more diverse chimeric libraries. DNA shuffling generates combinatorial libraries of chimeric genes by stochastically recombining parent genes. The resulting libraries are subjected to large-scale genetic selection or screening to identify those chimeras with favorable properties (e.g., enhanced stability or enzymatic activity). While DNA shuffling has been applied quite successfully, it is limited by its homology-dependent, stochastic nature. Consequently, it is used only with parents of sufficient overall sequence identity, and provides no control over the resulting chimeric library.BACKGROUNDDNA shuffling generates combinatorial libraries of chimeric genes by stochastically recombining parent genes. The resulting libraries are subjected to large-scale genetic selection or screening to identify those chimeras with favorable properties (e.g., enhanced stability or enzymatic activity). While DNA shuffling has been applied quite successfully, it is limited by its homology-dependent, stochastic nature. Consequently, it is used only with parents of sufficient overall sequence identity, and provides no control over the resulting chimeric library.This paper presents efficient methods to extend the scope of DNA shuffling to handle significantly more diverse parents and to generate more predictable, optimized libraries. Our CODNS (cross-over optimization for DNA shuffling) approach employs polynomial-time dynamic programming algorithms to select codons for the parental amino acids, allowing for zero or a fixed number of conservative substitutions. We first present efficient algorithms to optimize the local sequence identity or the nearest-neighbor approximation of the change in free energy upon annealing, objectives that were previously optimized by computationally-expensive integer programming methods. We then present efficient algorithms for more powerful objectives that seek to localize and enhance the frequency of recombination by producing "runs" of common nucleotides either overall or according to the sequence diversity of the resulting chimeras. We demonstrate the effectiveness of CODNS in choosing codons and allocating substitutions to promote recombination between parents targeted in earlier studies: two GAR transformylases (41% amino acid sequence identity), two very distantly related DNA polymerases, Pol X and β (15%), and beta-lactamases of varying identity (26-47%).RESULTSThis paper presents efficient methods to extend the scope of DNA shuffling to handle significantly more diverse parents and to generate more predictable, optimized libraries. Our CODNS (cross-over optimization for DNA shuffling) approach employs polynomial-time dynamic programming algorithms to select codons for the parental amino acids, allowing for zero or a fixed number of conservative substitutions. We first present efficient algorithms to optimize the local sequence identity or the nearest-neighbor approximation of the change in free energy upon annealing, objectives that were previously optimized by computationally-expensive integer programming methods. We then present efficient algorithms for more powerful objectives that seek to localize and enhance the frequency of recombination by producing "runs" of common nucleotides either overall or according to the sequence diversity of the resulting chimeras. We demonstrate the effectiveness of CODNS in choosing codons and allocating substitutions to promote recombination between parents targeted in earlier studies: two GAR transformylases (41% amino acid sequence identity), two very distantly related DNA polymerases, Pol X and β (15%), and beta-lactamases of varying identity (26-47%).Our methods provide the protein engineer with a new approach to DNA shuffling that supports substantially more diverse parents, is more deterministic, and generates more predictable and more diverse chimeric libraries.CONCLUSIONSOur methods provide the protein engineer with a new approach to DNA shuffling that supports substantially more diverse parents, is more deterministic, and generates more predictable and more diverse chimeric libraries. DNA shuffling generates combinatorial libraries of chimeric genes by stochastically recombining parent genes. The resulting libraries are subjected to large-scale genetic selection or screening to identify those chimeras with favorable properties (e.g., enhanced stability or enzymatic activity). While DNA shuffling has been applied quite successfully, it is limited by its homology-dependent, stochastic nature. Consequently, it is used only with parents of sufficient overall sequence identity, and provides no control over the resulting chimeric library. This paper presents efficient methods to extend the scope of DNA shuffling to handle significantly more diverse parents and to generate more predictable, optimized libraries. Our CODNS (cross-over optimization for DNA shuffling) approach employs polynomial-time dynamic programming algorithms to select codons for the parental amino acids, allowing for zero or a fixed number of conservative substitutions. We first present efficient algorithms to optimize the local sequence identity or the nearest-neighbor approximation of the change in free energy upon annealing, objectives that were previously optimized by computationally-expensive integer programming methods. We then present efficient algorithms for more powerful objectives that seek to localize and enhance the frequency of recombination by producing "runs" of common nucleotides either overall or according to the sequence diversity of the resulting chimeras. We demonstrate the effectiveness of CODNS in choosing codons and allocating substitutions to promote recombination between parents targeted in earlier studies: two GAR transformylases (41% amino acid sequence identity), two very distantly related DNA polymerases, Pol X and β (15%), and beta-lactamases of varying identity (26-47%). Our methods provide the protein engineer with a new approach to DNA shuffling that supports substantially more diverse parents, is more deterministic, and generates more predictable and more diverse chimeric libraries. Doc number: S3 Abstract Background: DNA shuffling generates combinatorial libraries of chimeric genes by stochastically recombining parent genes. The resulting libraries are subjected to large-scale genetic selection or screening to identify those chimeras with favorable properties (e.g., enhanced stability or enzymatic activity). While DNA shuffling has been applied quite successfully, it is limited by its homology-dependent, stochastic nature. Consequently, it is used only with parents of sufficient overall sequence identity, and provides no control over the resulting chimeric library. Results: This paper presents efficient methods to extend the scope of DNA shuffling to handle significantly more diverse parents and to generate more predictable, optimized libraries. Our CODNS (cross-over optimization for DNA shuffling) approach employs polynomial-time dynamic programming algorithms to select codons for the parental amino acids, allowing for zero or a fixed number of conservative substitutions. We first present efficient algorithms to optimize the local sequence identity or the nearest-neighbor approximation of the change in free energy upon annealing, objectives that were previously optimized by computationally-expensive integer programming methods. We then present efficient algorithms for more powerful objectives that seek to localize and enhance the frequency of recombination by producing "runs" of common nucleotides either overall or according to the sequence diversity of the resulting chimeras. We demonstrate the effectiveness of CODNS in choosing codons and allocating substitutions to promote recombination between parents targeted in earlier studies: two GAR transformylases (41% amino acid sequence identity), two very distantly related DNA polymerases, Pol X and β (15%), and beta-lactamases of varying identity (26-47%). Conclusions: Our methods provide the protein engineer with a new approach to DNA shuffling that supports substantially more diverse parents, is more deterministic, and generates more predictable and more diverse chimeric libraries. Background DNA shuffling generates combinatorial libraries of chimeric genes by stochastically recombining parent genes. The resulting libraries are subjected to large-scale genetic selection or screening to identify those chimeras with favorable properties (e.g., enhanced stability or enzymatic activity). While DNA shuffling has been applied quite successfully, it is limited by its homology-dependent, stochastic nature. Consequently, it is used only with parents of sufficient overall sequence identity, and provides no control over the resulting chimeric library. Results This paper presents efficient methods to extend the scope of DNA shuffling to handle significantly more diverse parents and to generate more predictable, optimized libraries. Our C ODNS (cross-over optimization for DNA shuffling) approach employs polynomial-time dynamic programming algorithms to select codons for the parental amino acids, allowing for zero or a fixed number of conservative substitutions. We first present efficient algorithms to optimize the local sequence identity or the nearest-neighbor approximation of the change in free energy upon annealing, objectives that were previously optimized by computationally-expensive integer programming methods. We then present efficient algorithms for more powerful objectives that seek to localize and enhance the frequency of recombination by producing "runs" of common nucleotides either overall or according to the sequence diversity of the resulting chimeras. We demonstrate the effectiveness of C ODNS in choosing codons and allocating substitutions to promote recombination between parents targeted in earlier studies: two GAR transformylases (41% amino acid sequence identity), two very distantly related DNA polymerases, Pol X and β (15%), and beta-lactamases of varying identity (26-47%). Conclusions Our methods provide the protein engineer with a new approach to DNA shuffling that supports substantially more diverse parents, is more deterministic, and generates more predictable and more diverse chimeric libraries. |
| ArticleNumber | S3 |
| Author | Friedman, Alan M Bailey-Kellogg, Chris He, Lu |
| Author_xml | – sequence: 1 givenname: Lu surname: He fullname: He, Lu organization: Dept of Computer Science, Dartmouth College – sequence: 2 givenname: Alan M surname: Friedman fullname: Friedman, Alan M email: afried@purdue.edu organization: Dept of Biological Sciences, Markey Center for Structural Biology, Purdue Cancer Center, and Bindley Bioscience Center, Purdue University – sequence: 3 givenname: Chris surname: Bailey-Kellogg fullname: Bailey-Kellogg, Chris email: cbk@cs.dartmouth.edu organization: Dept of Computer Science, Dartmouth College |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/22536901$$D View this record in MEDLINE/PubMed |
| BookMark | eNqNkUtPxCAUhYnRqDP6B1yYxpWbKhcopcuJ72SiC3VNWgojpi0jtCb666WOr7gwJjeBwHcOl3smaL1znUZoD_ARgODHwHJICeAsBZrejrWGtr8O13_st9AkhEeMIRc420RbhGSUFxi2EZ81C-dt_9CGxDifuGVvW_tqu0WivAshdc_ah8R2yen1LAkPgzFNvNxBG6Zsgt79WKfo_vzs7uQynd9cXJ3M5qliGfQpaEMYZwaLKlekYkKVWvMSVwUwo4DpqqhYbQypK5KbKnZXZDrnQtWFIapWdIoOV75L754GHXrZ2qB005SddkOQgKM_p5hm_0ABc8qpEBE9-IU-usF38SOyoMAE0AJHaP8DGqpW13LpbVv6F_k5uwiIFfA-KK-NVLYve-u63pe2iQ_KMSY5piDHFCRQeTtWlJJf0k_3P0V0JQoR7hbaf3f9h-oNWJmjTw |
| CitedBy_id | crossref_primary_10_1186_s13628_017_0036_7 crossref_primary_10_3390_molecules26247476 crossref_primary_10_1039_C4CS00351A crossref_primary_10_1177_1176934320924681 crossref_primary_10_1109_TCBB_2022_3175908 |
| Cites_doi | 10.1038/12884 10.1186/1471-2105-7-285 10.1073/pnas.051631498 10.1038/370389a0 10.1073/pnas.95.4.1460 10.1021/cc700106e 10.1038/7003 10.1093/nar/10.22.7055 10.1110/ps.0306603 10.1038/34663 10.1089/cmb.2009.0090 10.1016/0025-5564(85)90096-3 10.1089/cmb.2007.R016 10.1093/nar/30.11.2407 10.1038/nbt0309-220 10.1073/pnas.89.22.10915 10.1016/S0022-2836(02)00442-4 10.1093/nar/28.1.292 10.1002/prot.23237 10.1016/S0022-2836(02)00675-7 10.1089/cmb.1999.6.77 10.1073/pnas.91.22.10747 10.1073/pnas.0537968100 10.1038/70754 10.1002/prot.20984 10.1038/11737 10.1142/9781860948732_0008 10.1017/CBO9780511790492 10.1038/88129 10.1385/1-59259-395-X:85 |
| ContentType | Journal Article |
| Copyright | He et al.; licensee BioMed Central Ltd. 2012 This article is published under license to BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License ( ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. 2012 He et al.; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
| Copyright_xml | – notice: He et al.; licensee BioMed Central Ltd. 2012 This article is published under license to BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License ( ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. – notice: 2012 He et al.; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
| DBID | C6C AAYXX CITATION CGR CUY CVF ECM EIF NPM 3V. 7QO 7SC 7X7 7XB 88E 8AL 8AO 8FD 8FE 8FG 8FH 8FI 8FJ 8FK ABUWG AEUYN AFKRA ARAPS AZQEC BBNVY BENPR BGLVJ BHPHI CCPQU DWQXO FR3 FYUFA GHDGH GNUQQ HCIFZ JQ2 K7- K9. L7M LK8 L~C L~D M0N M0S M1P M7P P5Z P62 P64 PHGZM PHGZT PIMPY PJZUB PKEHL PPXIY PQEST PQGLB PQQKQ PQUKI PRINS Q9U 7X8 7TM |
| DOI | 10.1186/1471-2105-13-S3-S3 |
| DatabaseName | Springer Nature OA Free Journals CrossRef Medline MEDLINE MEDLINE (Ovid) MEDLINE MEDLINE PubMed ProQuest Central (Corporate) Biotechnology Research Abstracts Computer and Information Systems Abstracts Health & Medical Collection ProQuest Central (purchase pre-March 2016) Medical Database (Alumni Edition) Computing Database (Alumni Edition) ProQuest Pharma Collection Technology Research Database ProQuest SciTech Collection ProQuest Technology Collection ProQuest Natural Science Collection ProQuest Hospital Collection Hospital Premium Collection (Alumni Edition) ProQuest Central (Alumni) (purchase pre-March 2016) ProQuest Central (Alumni) ProQuest One Sustainability ProQuest Central UK/Ireland Advanced Technologies & Computer Science Collection ProQuest Central Essentials - QC Biological Science Collection AUTh Library subscriptions: ProQuest Central Technology collection Natural Science Collection ProQuest One ProQuest Central Korea Engineering Research Database Health Research Premium Collection Health Research Premium Collection (Alumni) ProQuest Central Student SciTech Premium Collection ProQuest Computer Science Collection Computer Science Database ProQuest Health & Medical Complete (Alumni) Advanced Technologies Database with Aerospace Biological Sciences Computer and Information Systems Abstracts Academic Computer and Information Systems Abstracts Professional Computing Database ProQuest Health & Medical Collection Medical Database Biological Science Database Advanced Technologies & Aerospace Database ProQuest Advanced Technologies & Aerospace Collection Biotechnology and BioEngineering Abstracts Proquest Central Premium ProQuest One Academic (New) ProQuest 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) One Applied & Life Sciences ProQuest One Academic (retired) ProQuest One Academic UKI Edition ProQuest Central China ProQuest Central Basic MEDLINE - Academic Nucleic Acids Abstracts |
| DatabaseTitle | CrossRef MEDLINE Medline Complete MEDLINE with Full Text PubMed MEDLINE (Ovid) Publicly Available Content Database Computer Science Database ProQuest Central Student ProQuest Advanced Technologies & Aerospace Collection ProQuest Central Essentials ProQuest Computer Science Collection Computer and Information Systems Abstracts SciTech Premium Collection ProQuest Central China ProQuest One Applied & Life Sciences ProQuest One Sustainability Health Research Premium Collection Natural Science Collection Health & Medical Research Collection Biological Science Collection ProQuest Central (New) ProQuest Medical Library (Alumni) Advanced Technologies & Aerospace Collection ProQuest Biological Science Collection ProQuest One Academic Eastern Edition ProQuest Hospital Collection ProQuest Technology Collection Health Research Premium Collection (Alumni) Biological Science Database ProQuest Hospital Collection (Alumni) Biotechnology and BioEngineering Abstracts ProQuest Health & Medical Complete ProQuest One Academic UKI Edition Engineering Research Database ProQuest One Academic ProQuest One Academic (New) Technology Collection Technology Research Database Computer and Information Systems Abstracts – Academic 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 Pharma Collection ProQuest Central ProQuest Health & Medical Research Collection Biotechnology Research Abstracts Health and Medicine Complete (Alumni Edition) ProQuest Central Korea Advanced Technologies Database with Aerospace ProQuest Computing ProQuest Central Basic ProQuest Computing (Alumni Edition) ProQuest SciTech Collection Computer and Information Systems Abstracts Professional Advanced Technologies & Aerospace Database ProQuest Medical Library ProQuest Central (Alumni) MEDLINE - Academic Nucleic Acids Abstracts |
| DatabaseTitleList | Engineering Research Database MEDLINE - Academic MEDLINE Publicly Available Content Database |
| 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: PIMPY name: ProQuest Publicly Available Content Database url: http://search.proquest.com/publiccontent sourceTypes: Aggregation Database |
| DeliveryMethod | fulltext_linktorsrc |
| Discipline | Biology |
| EISSN | 1471-2105 |
| EndPage | S3 |
| ExternalDocumentID | 2614904731 22536901 10_1186_1471_2105_13_S3_S3 |
| Genre | Research Support, U.S. Gov't, Non-P.H.S Journal Article |
| GroupedDBID | --- 0R~ 23N 2VQ 2WC 4.4 53G 5VS 6J9 7X7 88E 8AO 8FE 8FG 8FH 8FI 8FJ AAFWJ AAJSJ AAKPC AASML ABDBF ABUWG ACGFO ACGFS ACIHN ACIWK ACPRK ACUHS ADBBV ADMLS ADRAZ ADUKV AEAQA AENEX AEUYN AFKRA AFPKN AFRAH AHBYD AHMBA AHSBF AHYZX ALMA_UNASSIGNED_HOLDINGS AMKLP AMTXH AOIJS ARAPS AZQEC BAPOH BAWUL BBNVY BCNDV BENPR BFQNJ BGLVJ BHPHI BMC BPHCQ BVXVI C6C CCPQU CS3 DIK DU5 DWQXO E3Z EAD EAP EAS EBD EBLON EBS EJD EMB EMK EMOBN ESX F5P FYUFA GNUQQ GROUPED_DOAJ GX1 HCIFZ HMCUK HYE IAO ICD IHR INH INR IPNFZ ISR ITC K6V K7- KQ8 LK8 M1P M48 M7P MK~ ML0 M~E O5R O5S OK1 OVT P2P P62 PGMZT PHGZM PHGZT PIMPY PJZUB PPXIY PQGLB PQQKQ PROAC PSQYO PUEGO RBZ RIG RNS ROL RPM RSV SBL SOJ SV3 TR2 TUS UKHRP W2D WOQ WOW XH6 XSB AAYXX AFFHD CITATION ALIPV CGR CUY CVF ECM EIF NPM 3V. 7QO 7SC 7XB 8AL 8FD 8FK FR3 JQ2 K9. L7M L~C L~D M0N P64 PKEHL PQEST PQUKI PRINS Q9U 7X8 7TM |
| ID | FETCH-LOGICAL-c451t-1ef2464f08b7c2b48caee6a0b914fc14eb9b4dff2db27fb78095e768cd9f2cdc3 |
| IEDL.DBID | RSV |
| ISICitedReferencesCount | 6 |
| ISICitedReferencesURI | http://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=Summon&SrcAuth=ProQuest&DestLinkType=CitingArticles&DestApp=WOS_CPL&KeyUT=000303936300003&url=https%3A%2F%2Fcvtisr.summon.serialssolutions.com%2F%23%21%2Fsearch%3Fho%3Df%26include.ft.matches%3Dt%26l%3Dnull%26q%3D |
| ISSN | 1471-2105 |
| IngestDate | Mon Oct 06 18:06:41 EDT 2025 Sun Nov 09 12:13:50 EST 2025 Mon Oct 06 18:39:15 EDT 2025 Mon Jul 21 05:41:49 EDT 2025 Sat Nov 29 05:39:53 EST 2025 Tue Nov 18 22:18:57 EST 2025 Sat Sep 06 07:27:14 EDT 2025 |
| IsDoiOpenAccess | true |
| IsOpenAccess | true |
| IsPeerReviewed | true |
| IsScholarly | true |
| Issue | Suppl 3 |
| Keywords | Diversity Variance African Swine Fever Virus Codon Free Energy Dynamic Programming Algorithm |
| Language | English |
| LinkModel | DirectLink |
| MergedId | FETCHMERGED-LOGICAL-c451t-1ef2464f08b7c2b48caee6a0b914fc14eb9b4dff2db27fb78095e768cd9f2cdc3 |
| Notes | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 14 content type line 23 ObjectType-Article-2 ObjectType-Feature-1 ObjectType-Conference-3 SourceType-Conference Papers & Proceedings-2 |
| OpenAccessLink | https://link.springer.com/10.1186/1471-2105-13-S3-S3 |
| PMID | 22536901 |
| PQID | 931481390 |
| PQPubID | 44065 |
| ParticipantIDs | proquest_miscellaneous_1024663035 proquest_miscellaneous_1010636388 proquest_journals_931481390 pubmed_primary_22536901 crossref_citationtrail_10_1186_1471_2105_13_S3_S3 crossref_primary_10_1186_1471_2105_13_S3_S3 springer_journals_10_1186_1471_2105_13_S3_S3 |
| PublicationCentury | 2000 |
| PublicationDate | 2012-03-21 |
| PublicationDateYYYYMMDD | 2012-03-21 |
| PublicationDate_xml | – month: 03 year: 2012 text: 2012-03-21 day: 21 |
| PublicationDecade | 2010 |
| PublicationPlace | London |
| PublicationPlace_xml | – name: London – name: England |
| PublicationTitle | BMC bioinformatics |
| PublicationTitleAbbrev | BMC Bioinformatics |
| PublicationTitleAlternate | BMC Bioinformatics |
| PublicationYear | 2012 |
| Publisher | BioMed Central Springer Nature B.V |
| Publisher_xml | – name: BioMed Central – name: Springer Nature B.V |
| References | PE O'Maille (5081_CR10) 2002; 321 L He (5081_CR29) 2012; 80 WPC Stemmer (5081_CR1) 1994; 370 WPC Stemmer (5081_CR2) 1994; 91 A Villalobos (5081_CR25) 2006; 7 A Crameri (5081_CR4) 1998; 391 MM Meyer (5081_CR11) 2003; 12 M Guoy (5081_CR27) 1982; 10 L Saftalov (5081_CR15) 2006; 64 V Sieber (5081_CR9) 2001; 19 C Littlehales (5081_CR3) 2009; 27 F Sun (5081_CR21) 1999; 6 N Maheshri (5081_CR23) 2003; 100 R Durbin (5081_CR19) 1998 MS Waterman (5081_CR28) 1985; 77 Y Nakamura (5081_CR26) 2000; 28 GL Moore (5081_CR22) 2001; 98 X Ye (5081_CR12) 2007; 14 F Christians (5081_CR7) 1999; 17 J SantaLucia Jr (5081_CR24) 1998; 95 C Chang (5081_CR5) 1999; 17 M Ostermeier (5081_CR8) 1999; 17 S Henikoff (5081_CR18) 1992; 89 G Moore (5081_CR17) 2002; 30 R Guerois (5081_CR20) 2002; 320 L Avramova (5081_CR16) 2008; 10 J Joern (5081_CR30) 2003 J Ness (5081_CR6) 1999; 17 W Zheng (5081_CR14) 2009; 16 W Zheng (5081_CR13) 2007; 6 |
| References_xml | – volume: 17 start-page: 893 year: 1999 ident: 5081_CR6 publication-title: Nat Biotechnol doi: 10.1038/12884 – volume: 7 start-page: 285 year: 2006 ident: 5081_CR25 publication-title: BMC Bioinformatics doi: 10.1186/1471-2105-7-285 – volume: 98 start-page: 3226 year: 2001 ident: 5081_CR22 publication-title: Proc Natl Acad Sci USA doi: 10.1073/pnas.051631498 – volume: 370 start-page: 389 year: 1994 ident: 5081_CR1 publication-title: Nature doi: 10.1038/370389a0 – volume: 95 start-page: 1460 year: 1998 ident: 5081_CR24 publication-title: Proc Natl Acad Sci USA doi: 10.1073/pnas.95.4.1460 – volume: 10 start-page: 63 year: 2008 ident: 5081_CR16 publication-title: J Comb Chem doi: 10.1021/cc700106e – volume: 17 start-page: 259 year: 1999 ident: 5081_CR7 publication-title: Nat Biotechnol doi: 10.1038/7003 – volume: 10 start-page: 7055 year: 1982 ident: 5081_CR27 publication-title: Nucleic Acids Res doi: 10.1093/nar/10.22.7055 – volume: 12 start-page: 1686 year: 2003 ident: 5081_CR11 publication-title: Protein Sci doi: 10.1110/ps.0306603 – volume: 391 start-page: 288 year: 1998 ident: 5081_CR4 publication-title: Nature doi: 10.1038/34663 – volume: 16 start-page: 1151 year: 2009 ident: 5081_CR14 publication-title: J Comput Biol doi: 10.1089/cmb.2009.0090 – volume: 77 start-page: 179 year: 1985 ident: 5081_CR28 publication-title: Math Biosci doi: 10.1016/0025-5564(85)90096-3 – volume: 14 start-page: 777 year: 2007 ident: 5081_CR12 publication-title: J Comput Biol doi: 10.1089/cmb.2007.R016 – volume: 30 start-page: 2407 year: 2002 ident: 5081_CR17 publication-title: Nucleic Acids Res doi: 10.1093/nar/30.11.2407 – volume: 27 start-page: 220 year: 2009 ident: 5081_CR3 publication-title: Nat Biotechnol doi: 10.1038/nbt0309-220 – volume: 89 start-page: 10915 year: 1992 ident: 5081_CR18 publication-title: Proc Natl Acad Sci USA doi: 10.1073/pnas.89.22.10915 – volume: 320 start-page: 369 year: 2002 ident: 5081_CR20 publication-title: J Mol Biol doi: 10.1016/S0022-2836(02)00442-4 – volume: 28 start-page: 292 year: 2000 ident: 5081_CR26 publication-title: Nucleic Acids Res doi: 10.1093/nar/28.1.292 – volume: 80 start-page: 790 issue: 3 year: 2012 ident: 5081_CR29 publication-title: Proteins doi: 10.1002/prot.23237 – volume: 321 start-page: 677 year: 2002 ident: 5081_CR10 publication-title: J Mol Biol doi: 10.1016/S0022-2836(02)00675-7 – volume: 6 start-page: 77 year: 1999 ident: 5081_CR21 publication-title: J Comput Biol doi: 10.1089/cmb.1999.6.77 – volume: 91 start-page: 10747 year: 1994 ident: 5081_CR2 publication-title: Proc Natl Acad Sci USA doi: 10.1073/pnas.91.22.10747 – volume: 100 start-page: 3071 year: 2003 ident: 5081_CR23 publication-title: Proc Natl Acad Sci USA doi: 10.1073/pnas.0537968100 – volume: 17 start-page: 1205 year: 1999 ident: 5081_CR8 publication-title: Nat Biotechnol doi: 10.1038/70754 – volume: 64 start-page: 629 issue: 3 year: 2006 ident: 5081_CR15 publication-title: Proteins doi: 10.1002/prot.20984 – volume: 17 start-page: 793 year: 1999 ident: 5081_CR5 publication-title: Nat Biotechnol doi: 10.1038/11737 – volume: 6 start-page: 31 year: 2007 ident: 5081_CR13 publication-title: Comput Syst Bioinformatics Conf doi: 10.1142/9781860948732_0008 – volume-title: Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids year: 1998 ident: 5081_CR19 doi: 10.1017/CBO9780511790492 – volume: 19 start-page: 456 year: 2001 ident: 5081_CR9 publication-title: Nat Biotechnol doi: 10.1038/88129 – start-page: 85 volume-title: Directed Evolution Library Creation: Methods and Protocols year: 2003 ident: 5081_CR30 doi: 10.1385/1-59259-395-X:85 |
| SSID | ssj0017805 |
| Score | 2.0551453 |
| Snippet | Background
DNA shuffling generates combinatorial libraries of chimeric genes by stochastically recombining parent genes. The resulting libraries are subjected... DNA shuffling generates combinatorial libraries of chimeric genes by stochastically recombining parent genes. The resulting libraries are subjected to... Doc number: S3 Abstract Background: DNA shuffling generates combinatorial libraries of chimeric genes by stochastically recombining parent genes. The resulting... Background: DNA shuffling generates combinatorial libraries of chimeric genes by stochastically recombining parent genes. The resulting libraries are subjected... |
| SourceID | proquest pubmed crossref springer |
| SourceType | Aggregation Database Index Database Enrichment Source Publisher |
| StartPage | S3 |
| SubjectTerms | African Swine Fever Virus - enzymology Algorithms Amino Acid Sequence Amino acid substitution Amino acids Animals Bacteria - enzymology beta-Lactamases - chemistry beta-Lactamases - genetics Bioinformatics Biology Biomedical and Life Sciences Chimeras Codon Codons Combinatorial libraries Computational Biology/Bioinformatics Computer Appl. in Life Sciences Computer applications Conferences Deoxyribonucleic acid DNA DNA Shuffling DNA-directed DNA polymerase E coli Engineers Enzymatic activity Escherichia coli - enzymology Free energy Gene Library Humans Integer programming Libraries Life Sciences Methods Microarrays Nearest-neighbor Nucleotide sequence Oligonucleotides Phosphoribosylglycinamide Formyltransferase - genetics Proceedings Protein Engineering - methods Rats Recombination Sequence Alignment Software Stochasticity Studies transformylase |
| SummonAdditionalLinks | – databaseName: Biological Science Database dbid: M7P link: http://cvtisr.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwpV1LT9wwEB7xaKVeeJTShkeVSr0Vi9hxvPYJrXiopxUSVOIWxY4NK0GWkt1K5dczk02CEGIvSLnFdkbj8fhzZjwfwE-HhmHLIrBgbMKkkQmzSitWWoo6cVMoUTZkE4PRSF9dmfM2N6du0yo7n9g46nLi6B_5oUkRuCNcSY7u_zIijaLgasugsQyrVCRBNJl7530Qgcr1d_dktDrk6IcZnnAyxlN2Qc_LvegVwHwVHG32nLP1d0q7AWst2IyHc-vYhCVffYaPc_rJ_1ughrfX2Gt6c1fHiF3jCbqPu_EjihI3AjNK76zjcRWfjIZxfTMLgS6vf4E_Z6eXx79Zy6PAnMz4lHEfhFQyJNoOnLBSu8J7VSTWcBkcl94aK8sQRGnFIFhUm8k8HkNcaYJwpUu3YaWaVP4bxDqTXuAoSeEGMqigE2lllhU-LVKOQ0bAO43mri0yTlwXt3lz2NAqp1nIaRZynuYX9ETwq-9zPy-xsbD1bqfxvF1udd6rO4If_VtcJxT8KCo_mdWUyoZoDL2NXtQG9aRwU88i-Dq3gV4i9HspkXdFcNAZxfP33xZ3Z6G4u_AJAZignDbB92Bl-jDz-_DB_ZuO64fvjTU_AYsV-nk priority: 102 providerName: ProQuest |
| Title | Algorithms for optimizing cross-overs in DNA shuffling |
| URI | https://link.springer.com/article/10.1186/1471-2105-13-S3-S3 https://www.ncbi.nlm.nih.gov/pubmed/22536901 https://www.proquest.com/docview/931481390 https://www.proquest.com/docview/1010636388 https://www.proquest.com/docview/1024663035 |
| Volume | 13 |
| WOSCitedRecordID | wos000303936300003&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 customDbUrl: eissn: 1471-2105 dateEnd: 99991231 omitProxy: false ssIdentifier: ssj0017805 issn: 1471-2105 databaseCode: RBZ dateStart: 20000101 isFulltext: true titleUrlDefault: https://www.biomedcentral.com/search/ providerName: BioMedCentral – providerCode: PRVAON databaseName: DOAJ Directory of Open Access Journals customDbUrl: eissn: 1471-2105 dateEnd: 99991231 omitProxy: false ssIdentifier: ssj0017805 issn: 1471-2105 databaseCode: DOA dateStart: 20000101 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: 1471-2105 dateEnd: 99991231 omitProxy: false ssIdentifier: ssj0017805 issn: 1471-2105 databaseCode: M~E dateStart: 20000101 isFulltext: true titleUrlDefault: https://road.issn.org providerName: ISSN International Centre – providerCode: PRVPQU databaseName: Advanced Technologies & Aerospace Database customDbUrl: eissn: 1471-2105 dateEnd: 99991231 omitProxy: false ssIdentifier: ssj0017805 issn: 1471-2105 databaseCode: P5Z dateStart: 20090101 isFulltext: true titleUrlDefault: https://search.proquest.com/hightechjournals providerName: ProQuest – providerCode: PRVPQU databaseName: Biological Science Database customDbUrl: eissn: 1471-2105 dateEnd: 99991231 omitProxy: false ssIdentifier: ssj0017805 issn: 1471-2105 databaseCode: M7P dateStart: 20090101 isFulltext: true titleUrlDefault: http://search.proquest.com/biologicalscijournals providerName: ProQuest – providerCode: PRVPQU databaseName: Computer Science Database customDbUrl: eissn: 1471-2105 dateEnd: 99991231 omitProxy: false ssIdentifier: ssj0017805 issn: 1471-2105 databaseCode: K7- dateStart: 20090101 isFulltext: true titleUrlDefault: http://search.proquest.com/compscijour providerName: ProQuest – providerCode: PRVPQU databaseName: Health & Medical Collection customDbUrl: eissn: 1471-2105 dateEnd: 99991231 omitProxy: false ssIdentifier: ssj0017805 issn: 1471-2105 databaseCode: 7X7 dateStart: 20090101 isFulltext: true titleUrlDefault: https://search.proquest.com/healthcomplete providerName: ProQuest – providerCode: PRVPQU databaseName: ProQuest Central customDbUrl: eissn: 1471-2105 dateEnd: 99991231 omitProxy: false ssIdentifier: ssj0017805 issn: 1471-2105 databaseCode: BENPR dateStart: 20090101 isFulltext: true titleUrlDefault: https://www.proquest.com/central providerName: ProQuest – providerCode: PRVPQU databaseName: ProQuest Publicly Available Content Database customDbUrl: eissn: 1471-2105 dateEnd: 99991231 omitProxy: false ssIdentifier: ssj0017805 issn: 1471-2105 databaseCode: PIMPY dateStart: 20090101 isFulltext: true titleUrlDefault: http://search.proquest.com/publiccontent providerName: ProQuest – providerCode: PRVAVX databaseName: SpringerLINK Contemporary 1997-Present customDbUrl: eissn: 1471-2105 dateEnd: 99991231 omitProxy: false ssIdentifier: ssj0017805 issn: 1471-2105 databaseCode: RSV dateStart: 20001201 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/eLvHCXMwnR1daxQxcOiHgi9aP3utXVbwTYObbDabPJ7aUhGPpady-rJssok9aPfK7Z2gv76T3O6JtBYshLzka5hkvjKTDMBLgwdD15UjTumEcMUTooUUpNbe60RVJVgdkk3ko5GcTFTRPQpr-2j33iUZOHUgayneUGSjBA2UjNCUjH3ZhG0Ud9InbDgZf137Dvwv_f3zmGvH_S2CruiVV3yiQdQcPbgdkDtwv1Mt4-HqLDyEDds8grurZJO_HoMYnv2YzaeL0_M2Rk01niGzOJ_-xtnjACfxwZxtPG3i96Nh3J4unfNP1Z_Al6PDz--OSZc1gRie0QWh1jEuuEukzg3TXJrKWlElWlHuDOVWK81r51itWe40YktlFo0OUyvHTG3Sp7DVzBq7C7HMuGU4S1KZnDvhZMI1z7LKplVKccoB0B6Rpem-FPeZLc7KYFpIUXp8lB4fJU3LsS8DeLUec7H6UOPG3vv9_pQdcbWlStGGQ80V13-xbkWq8K6OqrGzZesD11D3Qt4ib-qDeBIowrMBPFtt_Roi5HKpT9U1gNf9Pv9Z_9_g7v1f9324h_oX8yFtjD6HrcV8aQ_gjvm5mLbzCDbzSR5qGcH228NRcRKFKwOsP-Yk8mGqBdZF9h3biw-fim9RoIRLEdT6Cw |
| linkProvider | Springer Nature |
| linkToHtml | http://cvtisr.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMw1V1Lb9QwEB6VAioX3pRQHkaCE1iNHcdxDlW1olSttqyQWqTe3Nix6UpttjS7oPKf-h87TjZBqGJvPSD5FscZe8afP2fGHoB3Fg3DlIWnPjcxFbmIqZFK0tIErxPLC8nLJtlENhqpw8P86xJcdmdhQlhlh4kNUJcTG_6Rr-cJEnekK_Hm2Q8akkYF52qXQaO1iqG7-IU7tnpjdwvV-57z7c8Hn3boPKkAtSJlU8qc50IKHyuTWW6EsoVzsohNzoS3TDiTG1F6z0vDM28yhRzEISe3Ze65LW2C7d6C29iTLEyrYUZ7p0VID9Cdy1FynSHuU9xRpZQldD-Uv9e-a4T2mjO2WeO2H_xno_MQ7s_JNBm01v8Illz1GO626TUvnoAcnHxHKafHpzVBbk4mCI-n49_YddIMEA3hqzUZV2RrNCD18cz7cDj_KXy7EaGfwXI1qdxzICoVjmMrcWEz4aVXsTAiTQuXFAnDJiNgnQa1nV-iHnJ5nOhmM6WkDlrXQeuaJXo_lAg-9O-ctVeILKy91mlYz-Gk1r16I3jbP0UcCM6donKTWR1C9ZBtIpqqRXVwnCSSljSC1dbmeokQ15OQnCyCj50R_vn-v8V9sVDcN7Cyc_BlT-_tjoZrcA_JJg_xe5y9hOXp-cy9gjv253Rcn79uZhKBo5s2ziuCVlrz |
| linkToPdf | http://cvtisr.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwpR1dSxwxcLBaS1_Uaj_OzxX61gY32WwueTyqh6IcwrXiW9hkEz3QPbndK7S_vpPd27NiFaSQt3wNk5nJDPMF8NkiYZg888QrExOueEyMkILkJnidqMoEy-tmE93BQF5eqvO_svjraPfWJdnkNIQqTUV1cJf7hsWlOKAoUgkaKymhCRmG8QqWeAikD_b68GLuRwgV-9tUmX_ue_gdPdIxH_lH62-nv_r_AK_BykzljHoNjbyDBVesw3LThPLXBojezdV4Mqqub8sINdhojELkdvQbb4pqmEkI8iyjUREdDnpReT31PqSwv4cf_aPv347JrJsCsTylFaHOMy64j6XpWma4tJlzIouNotxbyp1Rhufes9ywrjeIOZU6NEZsrjyzuU0-wGIxLtwniGTKHcNT4sx2uRdextzwNM1ckiUUj-wAbZGq7azUeOh4caNrk0MKHfChAz40TfQwjA58me-5awptPLt6q30rPWO6UqsEbTvUaPH-_fkscktwgWSFG0_LENCGOhnKHPncGsSTwK897cDHhgzmEKH0S0ILrw58bd_8_v6nwd182fI9eHN-2NdnJ4PTLXiLKhoLUW-MbsNiNZm6HXhtf1ajcrJbE_sfH1f8_g |
| 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=Algorithms+for+optimizing+cross-overs+in+DNA+shuffling&rft.jtitle=BMC+bioinformatics&rft.au=He%2C+Lu&rft.au=Friedman%2C+Alan+M&rft.au=Bailey-Kellogg%2C+Chris&rft.date=2012-03-21&rft.pub=BioMed+Central&rft.eissn=1471-2105&rft.volume=13&rft.issue=Suppl+3&rft_id=info:doi/10.1186%2F1471-2105-13-S3-S3&rft.externalDocID=10_1186_1471_2105_13_S3_S3 |
| thumbnail_l | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/lc.gif&issn=1471-2105&client=summon |
| thumbnail_m | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/mc.gif&issn=1471-2105&client=summon |
| thumbnail_s | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/sc.gif&issn=1471-2105&client=summon |