{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2022,4,4]],"date-time":"2022-04-04T21:01:06Z","timestamp":1649106066279},"reference-count":27,"publisher":"Hindawi Limited","license":[{"start":{"date-parts":[[2012,1,1]],"date-time":"2012-01-01T00:00:00Z","timestamp":1325376000000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/3.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Applied Computational Intelligence and Soft Computing"],"published-print":{"date-parts":[[2012]]},"abstract":"<jats:p>To decode a long genome sequence, shotgun sequencing is the state-of-the-art technique. It needs to properly sequence a very large number, sometimes as large as millions, of short partially readable strings (fragments). Arranging those fragments in correct sequence is known as fragment assembling, which is an NP-problem. Presently used methods require enormous computational cost. In this work, we have shown how our modified genetic algorithm (GA) could solve this problem efficiently. In the proposed GA, the length of the chromosome, which represents the volume of the search space, is reduced with advancing generations, and thereby improves search efficiency. We also introduced a greedy mutation, by swapping nearby fragments using some heuristics, to improve the fitness of chromosomes. We compared results with Parsons\u2019 algorithm which is based on GA too. We used fragments with partial reads on both sides, mimicking fragments in real genome assembling process. In Parsons\u2019 work base-pair array of the whole fragment is known. Even then, we could obtain much better results, and we succeeded in restructuring contigs covering 100% of the genome sequences.<\/jats:p>","DOI":"10.1155\/2012\/945401","type":"journal-article","created":{"date-parts":[[2012,7,8]],"date-time":"2012-07-08T17:00:51Z","timestamp":1341766851000},"page":"1-11","source":"Crossref","is-referenced-by-count":3,"title":["An Efficient Genome Fragment Assembling Using GA with Neighborhood Aware Fitness Function"],"prefix":"10.1155","volume":"2012","author":[{"given":"Satoko","family":"Kikuchi","sequence":"first","affiliation":[{"name":"Faculty of Software and Information Science, Iwate Prefectural University, Takizawa-mura, Iwate 020-0193, Japan"}]},{"given":"Goutam","family":"Chakraborty","sequence":"additional","affiliation":[{"name":"Faculty of Software and Information Science, Iwate Prefectural University, Takizawa-mura, Iwate 020-0193, Japan"}]}],"member":"98","reference":[{"key":"13","year":"2004"},{"key":"2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btq108"},{"key":"3","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-11-S1-S20"},{"key":"19","doi-asserted-by":"publisher","DOI":"10.1038\/35057062"},{"key":"4","doi-asserted-by":"publisher","DOI":"10.1038\/nature03895"},{"key":"5","doi-asserted-by":"publisher","DOI":"10.1038\/171737a0"},{"key":"14","year":"2005"},{"key":"7","doi-asserted-by":"publisher","DOI":"10.1109\/MCAS.2004.1371584"},{"key":"6","doi-asserted-by":"publisher","DOI":"10.1038\/nature06936"},{"issue":"4","key":"17","doi-asserted-by":"crossref","first-page":"729","DOI":"10.1016\/0022-2836(82)90546-0","volume":"162","year":"1982","journal-title":"Journal of Molecular Biology"},{"key":"12","doi-asserted-by":"publisher","DOI":"10.1016\/S0065-2458(03)60006-9"},{"key":"15","year":"2003"},{"key":"20","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1089\/gst.1995.1.9","volume":"1","year":"1995","journal-title":"Genome Science and Technology"},{"key":"27","doi-asserted-by":"publisher","DOI":"10.1093\/dnares\/11.1.27"},{"key":"18","doi-asserted-by":"publisher","DOI":"10.1126\/science.287.5461.2196"},{"key":"21","doi-asserted-by":"publisher","DOI":"10.1101\/gr.9.9.868"},{"key":"23","doi-asserted-by":"publisher","DOI":"10.1007\/BF00993377"},{"key":"24","first-page":"600","volume":"1","year":"2003","journal-title":"IEEE Congress on Evolutionary Computation"},{"key":"26","doi-asserted-by":"publisher","DOI":"10.1166\/jctn.2005.004"},{"key":"9","doi-asserted-by":"publisher","DOI":"10.1006\/geno.1993.1180"},{"key":"1","doi-asserted-by":"publisher","DOI":"10.1126\/science.1058040"},{"key":"28","doi-asserted-by":"publisher","DOI":"10.1038\/nature04072"},{"key":"11","doi-asserted-by":"publisher","DOI":"10.1038\/nature05260"},{"key":"29","doi-asserted-by":"publisher","DOI":"10.1126\/science.1133609"},{"key":"30","year":"1997"},{"issue":"1","key":"32","doi-asserted-by":"crossref","first-page":"195","DOI":"10.1016\/0022-2836(81)90087-5","volume":"147","year":"1981","journal-title":"Journal of Molecular Biology"},{"key":"31","year":"1999"}],"container-title":["Applied Computational Intelligence and Soft Computing"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/downloads.hindawi.com\/journals\/acisc\/2012\/945401.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/downloads.hindawi.com\/journals\/acisc\/2012\/945401.xml","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/downloads.hindawi.com\/journals\/acisc\/2012\/945401.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2017,6,20]],"date-time":"2017-06-20T17:05:26Z","timestamp":1497978326000},"score":1,"resource":{"primary":{"URL":"http:\/\/www.hindawi.com\/journals\/acisc\/2012\/945401\/"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2012]]},"references-count":27,"alternative-id":["945401","945401"],"URL":"https:\/\/doi.org\/10.1155\/2012\/945401","relation":{},"ISSN":["1687-9724","1687-9732"],"issn-type":[{"value":"1687-9724","type":"print"},{"value":"1687-9732","type":"electronic"}],"subject":[],"published":{"date-parts":[[2012]]}}}