{"title":"克雷MTA-2的序列比对","authors":"S. Bokhari, J. Sauer","doi":"10.1109/IPDPS.2003.1213285","DOIUrl":null,"url":null,"abstract":"The standard algorithm for alignment of DNA sequences using dynamic programming has been implemented on the Cray MTA-2 (Multithreaded Architecture-2) at ENRI (Electronic Navigation Research Institute), Japan. Descriptions of several variants of this algorithm and their measured performance are provided. It is shown that the use of \"full/empty\" bits (a feature unique to the MTA) leads to implementations that provide almost perfect speedup for large problems on 1-8 processors. These results demonstrate the potential power of the MTA and emphasize its suitability for bioinformatic and dynamic programming applications.","PeriodicalId":177848,"journal":{"name":"Proceedings International Parallel and Distributed Processing Symposium","volume":"25 1","pages":"0"},"PeriodicalIF":0.0000,"publicationDate":"2003-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"13","resultStr":"{\"title\":\"Sequence alignment on the Cray MTA-2\",\"authors\":\"S. Bokhari, J. Sauer\",\"doi\":\"10.1109/IPDPS.2003.1213285\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"The standard algorithm for alignment of DNA sequences using dynamic programming has been implemented on the Cray MTA-2 (Multithreaded Architecture-2) at ENRI (Electronic Navigation Research Institute), Japan. Descriptions of several variants of this algorithm and their measured performance are provided. It is shown that the use of \\\"full/empty\\\" bits (a feature unique to the MTA) leads to implementations that provide almost perfect speedup for large problems on 1-8 processors. These results demonstrate the potential power of the MTA and emphasize its suitability for bioinformatic and dynamic programming applications.\",\"PeriodicalId\":177848,\"journal\":{\"name\":\"Proceedings International Parallel and Distributed Processing Symposium\",\"volume\":\"25 1\",\"pages\":\"0\"},\"PeriodicalIF\":0.0000,\"publicationDate\":\"2003-04-22\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"13\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Proceedings International Parallel and Distributed Processing Symposium\",\"FirstCategoryId\":\"1085\",\"ListUrlMain\":\"https://doi.org/10.1109/IPDPS.2003.1213285\",\"RegionNum\":0,\"RegionCategory\":null,\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"\",\"JCRName\":\"\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Proceedings International Parallel and Distributed Processing Symposium","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.1109/IPDPS.2003.1213285","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"","JCRName":"","Score":null,"Total":0}
The standard algorithm for alignment of DNA sequences using dynamic programming has been implemented on the Cray MTA-2 (Multithreaded Architecture-2) at ENRI (Electronic Navigation Research Institute), Japan. Descriptions of several variants of this algorithm and their measured performance are provided. It is shown that the use of "full/empty" bits (a feature unique to the MTA) leads to implementations that provide almost perfect speedup for large problems on 1-8 processors. These results demonstrate the potential power of the MTA and emphasize its suitability for bioinformatic and dynamic programming applications.
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