A Graph-Based Approach for the DNA Word Design Problem
The aim of this paper is to improve the best known solution of an important problem, the DNA Word Design problem, which has its roots in Bioinformatics and Coding Theory. The problem is to design DNA codes that satisfy some combinatorial constraints. The constraints considered are: minimum Hamming d...
Gespeichert in:
| Veröffentlicht in: | IEEE/ACM transactions on computational biology and bioinformatics 2021-11, Vol.18 (6), p.2747-2752 |
|---|---|
| Hauptverfasser: | , |
| Format: | Artikel |
| Sprache: | eng |
| Schlagworte: | |
| Online-Zugang: | Volltext bestellen |
| Tags: |
Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
|
| container_end_page | 2752 |
|---|---|
| container_issue | 6 |
| container_start_page | 2747 |
| container_title | IEEE/ACM transactions on computational biology and bioinformatics |
| container_volume | 18 |
| creator | Luncasu, Victor Raschip, Madalina |
| description | The aim of this paper is to improve the best known solution of an important problem, the DNA Word Design problem, which has its roots in Bioinformatics and Coding Theory. The problem is to design DNA codes that satisfy some combinatorial constraints. The constraints considered are: minimum Hamming distance, fixed GC content and the reverse complement Hamming distance. The problem is modeled as a maximum independent set problem. Existing complex approaches for the maximum independent set problem, suitable for large graphs, were tested. In order to tackle large instances, libraries for external memory computations and sampling techniques were investigated. Eventually, we succeed in finding good lower bounds for the instances that were analyzed. |
| doi_str_mv | 10.1109/TCBB.2020.3008346 |
| format | Article |
| fullrecord | <record><control><sourceid>proquest_RIE</sourceid><recordid>TN_cdi_pubmed_primary_32750888</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><ieee_id>9137668</ieee_id><sourcerecordid>2607896247</sourcerecordid><originalsourceid>FETCH-LOGICAL-c392t-1de068e35c624ca811b61825666b66447403a1add8089f20bd91f7edc4f243d83</originalsourceid><addsrcrecordid>eNpdkE1LAzEQhoMotlZ_gAiy4MXL1snHzibHfmgVinqoeAzZTda2tN2adA_-e7O09uBpBuZ5h5eHkGsKfUpBPcxGw2GfAYM-B5Bc4Anp0izLU6VQnLa7yNJMIe-QixCWAEwoEOekw1megZSyS3CQTLzZztOhCc4mg-3W16acJ1Xtk93cJePXQfJZe5uMXVh8bZJ3Xxcrt74kZ5VZBXd1mD3y8fQ4Gz2n07fJy2gwTUuu2C6l1gFKx7MSmSiNpLRAKlmGiAWiELkAbqixVoJUFYPCKlrlzpaiYoJbyXvkfv831vpuXNjp9SKUbrUyG1c3QUcKEBlTENG7f-iybvwmttMMIZcqVsgjRfdU6esQvKv01i_Wxv9oCrqVqlupupWqD1Jj5vbwuSnWzh4TfxYjcLMHFs6541lRniNK_gtlFnah</addsrcrecordid><sourcetype>Aggregation Database</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>2607896247</pqid></control><display><type>article</type><title>A Graph-Based Approach for the DNA Word Design Problem</title><source>IEEE Electronic Library (IEL)</source><creator>Luncasu, Victor ; Raschip, Madalina</creator><creatorcontrib>Luncasu, Victor ; Raschip, Madalina</creatorcontrib><description>The aim of this paper is to improve the best known solution of an important problem, the DNA Word Design problem, which has its roots in Bioinformatics and Coding Theory. The problem is to design DNA codes that satisfy some combinatorial constraints. The constraints considered are: minimum Hamming distance, fixed GC content and the reverse complement Hamming distance. The problem is modeled as a maximum independent set problem. Existing complex approaches for the maximum independent set problem, suitable for large graphs, were tested. In order to tackle large instances, libraries for external memory computations and sampling techniques were investigated. Eventually, we succeed in finding good lower bounds for the instances that were analyzed.</description><identifier>ISSN: 1545-5963</identifier><identifier>EISSN: 1557-9964</identifier><identifier>DOI: 10.1109/TCBB.2020.3008346</identifier><identifier>PMID: 32750888</identifier><identifier>CODEN: ITCBCY</identifier><language>eng</language><publisher>United States: IEEE</publisher><subject>Algorithms ; Base Composition - genetics ; Bioinformatics ; Combinatorial analysis ; Computational Biology - methods ; Computational modeling ; Computers, Molecular ; Deoxyribonucleic acid ; Design ; DNA ; DNA - chemistry ; DNA - genetics ; DNA - ultrastructure ; DNA computing ; DNA word design ; Evolutionary computation ; Genetic communication ; Hamming distance ; Lower bounds ; maximum independent set</subject><ispartof>IEEE/ACM transactions on computational biology and bioinformatics, 2021-11, Vol.18 (6), p.2747-2752</ispartof><rights>Copyright The Institute of Electrical and Electronics Engineers, Inc. (IEEE) 2021</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c392t-1de068e35c624ca811b61825666b66447403a1add8089f20bd91f7edc4f243d83</citedby><cites>FETCH-LOGICAL-c392t-1de068e35c624ca811b61825666b66447403a1add8089f20bd91f7edc4f243d83</cites><orcidid>0000-0003-0020-636X</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktohtml>$$Uhttps://ieeexplore.ieee.org/document/9137668$$EHTML$$P50$$Gieee$$H</linktohtml><link.rule.ids>314,776,780,792,27901,27902,54733</link.rule.ids><linktorsrc>$$Uhttps://ieeexplore.ieee.org/document/9137668$$EView_record_in_IEEE$$FView_record_in_$$GIEEE</linktorsrc><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/32750888$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Luncasu, Victor</creatorcontrib><creatorcontrib>Raschip, Madalina</creatorcontrib><title>A Graph-Based Approach for the DNA Word Design Problem</title><title>IEEE/ACM transactions on computational biology and bioinformatics</title><addtitle>TCBB</addtitle><addtitle>IEEE/ACM Trans Comput Biol Bioinform</addtitle><description>The aim of this paper is to improve the best known solution of an important problem, the DNA Word Design problem, which has its roots in Bioinformatics and Coding Theory. The problem is to design DNA codes that satisfy some combinatorial constraints. The constraints considered are: minimum Hamming distance, fixed GC content and the reverse complement Hamming distance. The problem is modeled as a maximum independent set problem. Existing complex approaches for the maximum independent set problem, suitable for large graphs, were tested. In order to tackle large instances, libraries for external memory computations and sampling techniques were investigated. Eventually, we succeed in finding good lower bounds for the instances that were analyzed.</description><subject>Algorithms</subject><subject>Base Composition - genetics</subject><subject>Bioinformatics</subject><subject>Combinatorial analysis</subject><subject>Computational Biology - methods</subject><subject>Computational modeling</subject><subject>Computers, Molecular</subject><subject>Deoxyribonucleic acid</subject><subject>Design</subject><subject>DNA</subject><subject>DNA - chemistry</subject><subject>DNA - genetics</subject><subject>DNA - ultrastructure</subject><subject>DNA computing</subject><subject>DNA word design</subject><subject>Evolutionary computation</subject><subject>Genetic communication</subject><subject>Hamming distance</subject><subject>Lower bounds</subject><subject>maximum independent set</subject><issn>1545-5963</issn><issn>1557-9964</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2021</creationdate><recordtype>article</recordtype><sourceid>RIE</sourceid><sourceid>EIF</sourceid><recordid>eNpdkE1LAzEQhoMotlZ_gAiy4MXL1snHzibHfmgVinqoeAzZTda2tN2adA_-e7O09uBpBuZ5h5eHkGsKfUpBPcxGw2GfAYM-B5Bc4Anp0izLU6VQnLa7yNJMIe-QixCWAEwoEOekw1megZSyS3CQTLzZztOhCc4mg-3W16acJ1Xtk93cJePXQfJZe5uMXVh8bZJ3Xxcrt74kZ5VZBXd1mD3y8fQ4Gz2n07fJy2gwTUuu2C6l1gFKx7MSmSiNpLRAKlmGiAWiELkAbqixVoJUFYPCKlrlzpaiYoJbyXvkfv831vpuXNjp9SKUbrUyG1c3QUcKEBlTENG7f-iybvwmttMMIZcqVsgjRfdU6esQvKv01i_Wxv9oCrqVqlupupWqD1Jj5vbwuSnWzh4TfxYjcLMHFs6541lRniNK_gtlFnah</recordid><startdate>20211101</startdate><enddate>20211101</enddate><creator>Luncasu, Victor</creator><creator>Raschip, Madalina</creator><general>IEEE</general><general>The Institute of Electrical and Electronics Engineers, Inc. (IEEE)</general><scope>97E</scope><scope>RIA</scope><scope>RIE</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7QF</scope><scope>7QO</scope><scope>7QQ</scope><scope>7SC</scope><scope>7SE</scope><scope>7SP</scope><scope>7SR</scope><scope>7TA</scope><scope>7TB</scope><scope>7U5</scope><scope>8BQ</scope><scope>8FD</scope><scope>F28</scope><scope>FR3</scope><scope>H8D</scope><scope>JG9</scope><scope>JQ2</scope><scope>KR7</scope><scope>L7M</scope><scope>L~C</scope><scope>L~D</scope><scope>P64</scope><scope>7X8</scope><orcidid>https://orcid.org/0000-0003-0020-636X</orcidid></search><sort><creationdate>20211101</creationdate><title>A Graph-Based Approach for the DNA Word Design Problem</title><author>Luncasu, Victor ; Raschip, Madalina</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c392t-1de068e35c624ca811b61825666b66447403a1add8089f20bd91f7edc4f243d83</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2021</creationdate><topic>Algorithms</topic><topic>Base Composition - genetics</topic><topic>Bioinformatics</topic><topic>Combinatorial analysis</topic><topic>Computational Biology - methods</topic><topic>Computational modeling</topic><topic>Computers, Molecular</topic><topic>Deoxyribonucleic acid</topic><topic>Design</topic><topic>DNA</topic><topic>DNA - chemistry</topic><topic>DNA - genetics</topic><topic>DNA - ultrastructure</topic><topic>DNA computing</topic><topic>DNA word design</topic><topic>Evolutionary computation</topic><topic>Genetic communication</topic><topic>Hamming distance</topic><topic>Lower bounds</topic><topic>maximum independent set</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Luncasu, Victor</creatorcontrib><creatorcontrib>Raschip, Madalina</creatorcontrib><collection>IEEE All-Society Periodicals Package (ASPP) 2005-present</collection><collection>IEEE All-Society Periodicals Package (ASPP) 1998-Present</collection><collection>IEEE Electronic Library (IEL)</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Aluminium Industry Abstracts</collection><collection>Biotechnology Research Abstracts</collection><collection>Ceramic Abstracts</collection><collection>Computer and Information Systems Abstracts</collection><collection>Corrosion Abstracts</collection><collection>Electronics & Communications Abstracts</collection><collection>Engineered Materials Abstracts</collection><collection>Materials Business File</collection><collection>Mechanical & Transportation Engineering Abstracts</collection><collection>Solid State and Superconductivity Abstracts</collection><collection>METADEX</collection><collection>Technology Research Database</collection><collection>ANTE: Abstracts in New Technology & Engineering</collection><collection>Engineering Research Database</collection><collection>Aerospace Database</collection><collection>Materials Research Database</collection><collection>ProQuest Computer Science Collection</collection><collection>Civil Engineering Abstracts</collection><collection>Advanced Technologies Database with Aerospace</collection><collection>Computer and Information Systems Abstracts Academic</collection><collection>Computer and Information Systems Abstracts Professional</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>IEEE/ACM transactions on computational biology and bioinformatics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext_linktorsrc</fulltext></delivery><addata><au>Luncasu, Victor</au><au>Raschip, Madalina</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>A Graph-Based Approach for the DNA Word Design Problem</atitle><jtitle>IEEE/ACM transactions on computational biology and bioinformatics</jtitle><stitle>TCBB</stitle><addtitle>IEEE/ACM Trans Comput Biol Bioinform</addtitle><date>2021-11-01</date><risdate>2021</risdate><volume>18</volume><issue>6</issue><spage>2747</spage><epage>2752</epage><pages>2747-2752</pages><issn>1545-5963</issn><eissn>1557-9964</eissn><coden>ITCBCY</coden><abstract>The aim of this paper is to improve the best known solution of an important problem, the DNA Word Design problem, which has its roots in Bioinformatics and Coding Theory. The problem is to design DNA codes that satisfy some combinatorial constraints. The constraints considered are: minimum Hamming distance, fixed GC content and the reverse complement Hamming distance. The problem is modeled as a maximum independent set problem. Existing complex approaches for the maximum independent set problem, suitable for large graphs, were tested. In order to tackle large instances, libraries for external memory computations and sampling techniques were investigated. Eventually, we succeed in finding good lower bounds for the instances that were analyzed.</abstract><cop>United States</cop><pub>IEEE</pub><pmid>32750888</pmid><doi>10.1109/TCBB.2020.3008346</doi><tpages>6</tpages><orcidid>https://orcid.org/0000-0003-0020-636X</orcidid><oa>free_for_read</oa></addata></record> |
| fulltext | fulltext_linktorsrc |
| identifier | ISSN: 1545-5963 |
| ispartof | IEEE/ACM transactions on computational biology and bioinformatics, 2021-11, Vol.18 (6), p.2747-2752 |
| issn | 1545-5963 1557-9964 |
| language | eng |
| recordid | cdi_pubmed_primary_32750888 |
| source | IEEE Electronic Library (IEL) |
| subjects | Algorithms Base Composition - genetics Bioinformatics Combinatorial analysis Computational Biology - methods Computational modeling Computers, Molecular Deoxyribonucleic acid Design DNA DNA - chemistry DNA - genetics DNA - ultrastructure DNA computing DNA word design Evolutionary computation Genetic communication Hamming distance Lower bounds maximum independent set |
| title | A Graph-Based Approach for the DNA Word Design Problem |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-02-09T03%3A05%3A20IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-proquest_RIE&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=A%20Graph-Based%20Approach%20for%20the%20DNA%20Word%20Design%20Problem&rft.jtitle=IEEE/ACM%20transactions%20on%20computational%20biology%20and%20bioinformatics&rft.au=Luncasu,%20Victor&rft.date=2021-11-01&rft.volume=18&rft.issue=6&rft.spage=2747&rft.epage=2752&rft.pages=2747-2752&rft.issn=1545-5963&rft.eissn=1557-9964&rft.coden=ITCBCY&rft_id=info:doi/10.1109/TCBB.2020.3008346&rft_dat=%3Cproquest_RIE%3E2607896247%3C/proquest_RIE%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=2607896247&rft_id=info:pmid/32750888&rft_ieee_id=9137668&rfr_iscdi=true |