An optimization approach to multiple sequence alignment
The problem of multiple sequence alignment is recast as an optimization problem using Markov decision theory. One seeks to minimize the expected or average cost of alignment subject to data-derived constraints. In this setting, the problem is equivalent to a linear program which can be solved effici...
Saved in:
| Published in | Applied mathematics letters Vol. 16; no. 5; pp. 785 - 790 |
|---|---|
| Main Authors | , , |
| Format | Journal Article |
| Language | English |
| Published |
Oxford
Elsevier Ltd
01.07.2003
Elsevier |
| Subjects | |
| Online Access | Get full text |
| ISSN | 0893-9659 1873-5452 |
| DOI | 10.1016/S0893-9659(03)00083-1 |
Cover
| Abstract | The problem of multiple sequence alignment is recast as an optimization problem using Markov decision theory. One seeks to minimize the expected or average cost of alignment subject to data-derived constraints. In this setting, the problem is equivalent to a linear program which can be solved efficiently using modern interior-point methods. We present numerical results from an implementation of the algorithm for protein sequence alignment |
|---|---|
| AbstractList | The problem of multiple sequence alignment is recast as an optimization problem using Markov decision theory. One seeks to minimize the expected or average cost of alignment subject to data-derived constraints. In this setting, the problem is equivalent to a linear program which can be solved efficiently using modern interior-point methods. We present numerical results from an implementation of the algorithm for protein sequence alignment |
| Author | Kearsley, A.J. Wan, Honghui Hunt, F.Y. |
| Author_xml | – sequence: 1 givenname: F.Y. surname: Hunt fullname: Hunt, F.Y. – sequence: 2 givenname: A.J. surname: Kearsley fullname: Kearsley, A.J. – sequence: 3 givenname: Honghui surname: Wan fullname: Wan, Honghui organization: National Center for Genome Research National Institutes of Health Bethesda, MD 20894, U.S.A |
| BackLink | http://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=14856388$$DView record in Pascal Francis |
| BookMark | eNqFkE9LwzAYh4MouE0_gtCLoIfqmyZpUzzIGP6DgQf1HGLyViNdWpNM0E9vt4mCl51-l-f5HZ4x2fWdR0KOKJxRoOX5A8ia5XUp6hNgpwAgWU53yIjKiuWCi2KXjH6RfTKO8W2AWM3kiFRTn3V9cgv3pZPrfKb7PnTavGapyxbLNrm-xSzi-xK9wUy37sUv0KcDstfoNuLhz07I0_XV4-w2n9_f3M2m89wwVqdccouW2ecKamzKhksUnHEKDa8MIOW24lJCyUVjC6atqFEIzSTqohIlQMEm5Hjz2-todNsE7Y2Lqg9uocOnolyKkkk5cGLDmdDFGLD5Q0CtKql1JbVKoICpdSVFB-_in2dcWpdIQbt2q325sXFI8OEwqGjcKpR1AU1StnNbHr4BB--Ciw |
| CitedBy_id | crossref_primary_10_2174_18750362_v16_e230306_2022_6 crossref_primary_10_1016_S1672_0229_06_60027_2 crossref_primary_10_2174_18750362_v16_230705_2023_7 |
| Cites_doi | 10.1089/cmb.1998.5.173 10.1287/ijoc.4.3.267 10.1016/0022-2836(70)90057-4 |
| ContentType | Journal Article |
| Copyright | 2003 2003 INIST-CNRS |
| Copyright_xml | – notice: 2003 – notice: 2003 INIST-CNRS |
| DBID | 6I. AAFTH AAYXX CITATION IQODW |
| DOI | 10.1016/S0893-9659(03)00083-1 |
| DatabaseName | ScienceDirect Open Access Titles Elsevier:ScienceDirect:Open Access CrossRef Pascal-Francis |
| DatabaseTitle | CrossRef |
| DatabaseTitleList | |
| DeliveryMethod | fulltext_linktorsrc |
| Discipline | Mathematics Applied Sciences |
| EISSN | 1873-5452 |
| EndPage | 790 |
| ExternalDocumentID | 14856388 10_1016_S0893_9659_03_00083_1 S0893965903000831 |
| GroupedDBID | --K --M .~1 0R~ 1B1 1RT 1~. 1~5 23M 4.4 457 4G. 5GY 5VS 6I. 7-5 71M 8P~ 9JN AACTN AAEDT AAEDW AAFTH AAIAV AAIKJ AAKOC AALRI AAOAW AAQFI AAQXK AAXUO ABAOU ABEFU ABFNM ABJNI ABMAC ABVKL ABXDB ABYKQ ACAZW ACDAQ ACGFS ACNNM ACRLP ADBBV ADEZE ADMUD ADTZH AEBSH AECPX AEKER AENEX AEXQZ AFFNX AFKWA AFTJW AGHFR AGUBO AGYEJ AHHHB AHJVU AIEXJ AIGVJ AIKHN AITUG AJBFU AJOXV ALMA_UNASSIGNED_HOLDINGS AMFUW AMRAJ ARUGR ASPBG AVWKF AXJTR AZFZN BJAXD BKOJK BLXMC CS3 EBS EFJIC EFLBG EJD EO8 EO9 EP2 EP3 F5P FDB FEDTE FGOYB FIRID FNPLU FYGXN G-2 G-Q GBLVA HVGLF HZ~ IHE IXB J1W JJJVA KOM M26 M41 MHUIS MO0 N9A NCXOZ O-L O9- OAUVE OK1 OZT P-8 P-9 P2P PC. Q38 R2- RIG RNS ROL RPZ SDF SDG SDP SES SEW SPC SPCBC SST SSW SSZ T5K UHS WUQ XPP ZMT ~G- AATTM AAXKI AAYWO AAYXX ABWVN ACRPL ACVFH ADCNI ADNMO ADVLN AEIPS AEUPX AFJKZ AFPUW AGCQF AGQPQ AGRNS AIGII AIIUN AKBMS AKRWK AKYEP ANKPU APXCP BNPGV CITATION SSH AFXIZ EFKBS IQODW |
| ID | FETCH-LOGICAL-c339t-84ded3db709ef6f48e543410f47c0e14d74880645fd23ad59e55a38ea27560023 |
| IEDL.DBID | .~1 |
| ISSN | 0893-9659 |
| IngestDate | Mon Jul 21 09:14:56 EDT 2025 Tue Jul 01 00:31:51 EDT 2025 Thu Apr 24 22:59:45 EDT 2025 Fri Feb 23 02:17:33 EST 2024 |
| IsDoiOpenAccess | true |
| IsOpenAccess | true |
| IsPeerReviewed | true |
| IsScholarly | true |
| Issue | 5 |
| Keywords | Linear programming Sequencing Alignment Markov decision Applied mathematics DNA Sequence alignment Optimization method Interior point method Algorithm |
| Language | English |
| License | http://www.elsevier.com/open-access/userlicense/1.0 https://www.elsevier.com/tdm/userlicense/1.0 https://www.elsevier.com/open-access/userlicense/1.0 CC BY 4.0 |
| LinkModel | DirectLink |
| MergedId | FETCHMERGED-LOGICAL-c339t-84ded3db709ef6f48e543410f47c0e14d74880645fd23ad59e55a38ea27560023 |
| OpenAccessLink | https://www.sciencedirect.com/science/article/pii/S0893965903000831 |
| PageCount | 6 |
| ParticipantIDs | pascalfrancis_primary_14856388 crossref_primary_10_1016_S0893_9659_03_00083_1 crossref_citationtrail_10_1016_S0893_9659_03_00083_1 elsevier_sciencedirect_doi_10_1016_S0893_9659_03_00083_1 |
| ProviderPackageCode | CITATION AAYXX |
| PublicationCentury | 2000 |
| PublicationDate | 2003-07-01 |
| PublicationDateYYYYMMDD | 2003-07-01 |
| PublicationDate_xml | – month: 07 year: 2003 text: 2003-07-01 day: 01 |
| PublicationDecade | 2000 |
| PublicationPlace | Oxford |
| PublicationPlace_xml | – name: Oxford |
| PublicationTitle | Applied mathematics letters |
| PublicationYear | 2003 |
| Publisher | Elsevier Ltd Elsevier |
| Publisher_xml | – name: Elsevier Ltd – name: Elsevier |
| References | Czyzyk, Mehrotra, Wright (BIB10) May 1996 Waterman (BIB5) 1995 Bixby (BIB11) 1992; 4 Korostensky, Gonnet (BIB1) 1998 Altman (BIB6) 1999 Chvátal (BIB9) 1983 Needleman, Wunsch (BIB3) 1970; 48 Durbin, Eddy, Krogh, Mitchison (BIB4) 1998 Ross (BIB7) 1970 Wright (BIB8) 1997 F. Hunt, A.J. Kearsley and A. O'Gallagher, Software for optimization-based multiple sequence alignment, Technical Report, Mathematical and Computational Science Division, National Institute of Standards and Technology, Gaithersburg, MD. Apostolico, Giancarlo (BIB2) 1998; 5 Wright (10.1016/S0893-9659(03)00083-1_BIB8) 1997 Czyzyk (10.1016/S0893-9659(03)00083-1_BIB10) 1996 Durbin (10.1016/S0893-9659(03)00083-1_BIB4) 1998 Chvátal (10.1016/S0893-9659(03)00083-1_BIB9) 1983 Bixby (10.1016/S0893-9659(03)00083-1_BIB11) 1992; 4 Needleman (10.1016/S0893-9659(03)00083-1_BIB3) 1970; 48 Apostolico (10.1016/S0893-9659(03)00083-1_BIB2) 1998; 5 Waterman (10.1016/S0893-9659(03)00083-1_BIB5) 1995 Altman (10.1016/S0893-9659(03)00083-1_BIB6) 1999 10.1016/S0893-9659(03)00083-1_BIB12 Korostensky (10.1016/S0893-9659(03)00083-1_BIB1) 1998 Ross (10.1016/S0893-9659(03)00083-1_BIB7) 1970 |
| References_xml | – year: 1998 ident: BIB4 article-title: Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids – volume: 5 start-page: 173 year: 1998 end-page: 196 ident: BIB2 article-title: Sequence alignment in molecular biology publication-title: J. Comput. Biol. – year: 1998 ident: BIB1 article-title: Gap Heuristics and Tree Construction Using Gaps – year: 1999 ident: BIB6 article-title: Constrained Markov Decision Processes – year: 1970 ident: BIB7 article-title: Applied Probability Models with Optimization Applications – year: 1983 ident: BIB9 article-title: Linear Programming – volume: 4 start-page: 267 year: 1992 end-page: 284 ident: BIB11 article-title: Implementing the simplex method: The initial basis publication-title: ORSA Journal on Computing – volume: 48 start-page: 443 year: 1970 end-page: 453 ident: BIB3 article-title: A general method applicable to the search for similarities in the amino acid sequence of two proteins publication-title: J. Mol. Bio. – year: 1997 ident: BIB8 article-title: Primal Dual Interior Point Methods – year: May 1996 ident: BIB10 publication-title: PCx User Guide, Technical Report OTC 96/01 – reference: F. Hunt, A.J. Kearsley and A. O'Gallagher, Software for optimization-based multiple sequence alignment, Technical Report, Mathematical and Computational Science Division, National Institute of Standards and Technology, Gaithersburg, MD. – year: 1995 ident: BIB5 article-title: Introduction to Computational Biology – ident: 10.1016/S0893-9659(03)00083-1_BIB12 – year: 1996 ident: 10.1016/S0893-9659(03)00083-1_BIB10 – year: 1997 ident: 10.1016/S0893-9659(03)00083-1_BIB8 – year: 1995 ident: 10.1016/S0893-9659(03)00083-1_BIB5 – year: 1999 ident: 10.1016/S0893-9659(03)00083-1_BIB6 – year: 1983 ident: 10.1016/S0893-9659(03)00083-1_BIB9 – year: 1998 ident: 10.1016/S0893-9659(03)00083-1_BIB1 – volume: 5 start-page: 173 issue: 2 year: 1998 ident: 10.1016/S0893-9659(03)00083-1_BIB2 article-title: Sequence alignment in molecular biology publication-title: J. Comput. Biol. doi: 10.1089/cmb.1998.5.173 – year: 1998 ident: 10.1016/S0893-9659(03)00083-1_BIB4 – year: 1970 ident: 10.1016/S0893-9659(03)00083-1_BIB7 – volume: 4 start-page: 267 year: 1992 ident: 10.1016/S0893-9659(03)00083-1_BIB11 article-title: Implementing the simplex method: The initial basis publication-title: ORSA Journal on Computing doi: 10.1287/ijoc.4.3.267 – volume: 48 start-page: 443 year: 1970 ident: 10.1016/S0893-9659(03)00083-1_BIB3 article-title: A general method applicable to the search for similarities in the amino acid sequence of two proteins publication-title: J. Mol. Bio. doi: 10.1016/0022-2836(70)90057-4 |
| SSID | ssj0003938 |
| Score | 1.6556616 |
| Snippet | The problem of multiple sequence alignment is recast as an optimization problem using Markov decision theory. One seeks to minimize the expected or average... |
| SourceID | pascalfrancis crossref elsevier |
| SourceType | Index Database Enrichment Source Publisher |
| StartPage | 785 |
| SubjectTerms | Alignment Applied sciences Biological and medical sciences Calculus of variations and optimal control Exact sciences and technology Fundamental and applied biological sciences. Psychology General aspects Linear programming Markov processes Mathematical analysis Mathematical programming Mathematics Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects) Operational research and scientific management Operational research. Management science Probability and statistics Probability theory and stochastic processes Sciences and techniques of general use Sequencing |
| Title | An optimization approach to multiple sequence alignment |
| URI | https://dx.doi.org/10.1016/S0893-9659(03)00083-1 |
| Volume | 16 |
| hasFullText | 1 |
| inHoldings | 1 |
| isFullTextHit | |
| isPrint | |
| link | http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwnV3PS8MwFA5jXhQRf-L8MXLwoIdszZq0yXEOx6ZsFx3sFtImkYF2w9Wrf7tJ2q7uIILHhrzX8vX1vRS-9z0AbozWmPFejIwt7vYHBVPEE5wgHBomqYoj5YXnJ9NoNCOPczpvgEHVC-NolWXuL3K6z9blSrdEs7taLLrPgS21Tg7Phqmfl-U62EnsYr3zVdM8Qu6nWbvNyO2uu3gKD37xNgjvvBOEf6tP-yu5tqiZYtzFjxo0PAQH5eER9ovnOwINnR2DvclGeXV9AuJ-Bpc2DbyX_ZWwEg2H-RJW7EFYEaihPYW_ej7AKZgNH14GI1QOR0BpGPIcMaK0cuLIAdcmMoRp1ySKA0PiNNCYqNh9mhGhRvVCqSjXlMqQaen03l2lPgPNbJnpcwCpjpSWSWoIlwQbLqVmUrppjkrrlEQtQCpIRFoqh7sBFm-ipohZJIVDUgSh8EgK3AKdjdmqkM74y4BVeIutGBA2vf9l2t56P_UNCaM2xbCL__u-BLuewec5ulegmX986mt7EsmTtg-1Ntjpj59GU3s1nt9_A1mn1_g |
| linkProvider | Elsevier |
| linkToHtml | http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwnV3PT8IwGG0QD2qM8WfEH9iDBz1MVtpu7RGNBBS4CAm3pqytIdFBZP7_tt0GcjAkXpu2W167931L3vc-AG6N1ojxZhwYG9ztDwqiAZ-gSYCwYZKqOFLeeL4_iDoj8jKm4wp4KmthnKyy4P6c0z1bFyONAs3GfDptvIU21Do7PHtNfb-sLbBts4HIGeh3x49LOsbct7N2swM3fVXGk2_hB-9CfO93CdBfAWp_LhcWNpP3u_gVhNqH4KDIHmErf8EjUNHpMdjrL61XFycgbqVwZnngsyiwhKVrOMxmsJQPwlJBDW0a_u4FAadg1H4ePnWCojtCkGDMs4ARpZVzRw65NpEhTLsqURQaEiehRkTF7tuMCDWqiaWiXFMqMdPSGb67UH0Gquks1ecAUh0pLSeJIVwSZLiUmknp2jkqrRMS1QApIRFJYR3uOlh8iJVGzCIpHJIixMIjKVANPCyXzXPvjE0LWIm3WLsEwvL7pqX1tfNZPZAwajmGXfx_7xuw0xn2e6LXHbxegl0v5_OC3StQzb6-9bVNS7JJ3V-7H3zX2JQ |
| 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=An+optimization+approach+to+multiple+sequence+alignment&rft.jtitle=Applied+mathematics+letters&rft.au=Hunt%2C+F.Y.&rft.au=Kearsley%2C+A.J.&rft.au=Wan%2C+Honghui&rft.date=2003-07-01&rft.pub=Elsevier+Ltd&rft.issn=0893-9659&rft.eissn=1873-5452&rft.volume=16&rft.issue=5&rft.spage=785&rft.epage=790&rft_id=info:doi/10.1016%2FS0893-9659%2803%2900083-1&rft.externalDocID=S0893965903000831 |
| thumbnail_l | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/lc.gif&issn=0893-9659&client=summon |
| thumbnail_m | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/mc.gif&issn=0893-9659&client=summon |
| thumbnail_s | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/sc.gif&issn=0893-9659&client=summon |