{"title":"CoMRI:用于序列相似性查询的压缩多分辨率索引结构","authors":"Hong Sun, Ozgur Ozturk, H. Ferhatosmanoğlu","doi":"10.1109/CSB.2003.1227406","DOIUrl":null,"url":null,"abstract":"In this paper, we present CoMRI, compressed multiresolution index, our system for fast sequence similarity search in DNA sequence databases. We employ virtual bounding rectangle (VBR) concept to build a compressed, grid style index structure. An advantage of grid format over trees is subsequence location information is given by the order of corresponding VBR in the VBR list. Taking advantage of VBRs, our index structure fits into a reasonable size of memory easily. Together with a new optimized multiresolution search algorithm, the query speed is improved significantly. Extensive performance evaluations on human chromosome sequence data show that VBRs save 80%-93% index storage size compared to MBRs (minimum bounding rectangles) and new search algorithm prunes almost all unnecessary VBRs which guarantees efficient disk I/O and CPU cost. According to the results of our experiments, the performance of CoMRI is at least 100 times faster than MRS which is another grid index structure introduced very recently.","PeriodicalId":147883,"journal":{"name":"Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003","volume":"31 1","pages":"0"},"PeriodicalIF":0.0000,"publicationDate":"2003-08-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"7","resultStr":"{\"title\":\"CoMRI: a compressed multiresolution index structure for sequence similarity queries\",\"authors\":\"Hong Sun, Ozgur Ozturk, H. Ferhatosmanoğlu\",\"doi\":\"10.1109/CSB.2003.1227406\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"In this paper, we present CoMRI, compressed multiresolution index, our system for fast sequence similarity search in DNA sequence databases. We employ virtual bounding rectangle (VBR) concept to build a compressed, grid style index structure. An advantage of grid format over trees is subsequence location information is given by the order of corresponding VBR in the VBR list. Taking advantage of VBRs, our index structure fits into a reasonable size of memory easily. Together with a new optimized multiresolution search algorithm, the query speed is improved significantly. Extensive performance evaluations on human chromosome sequence data show that VBRs save 80%-93% index storage size compared to MBRs (minimum bounding rectangles) and new search algorithm prunes almost all unnecessary VBRs which guarantees efficient disk I/O and CPU cost. According to the results of our experiments, the performance of CoMRI is at least 100 times faster than MRS which is another grid index structure introduced very recently.\",\"PeriodicalId\":147883,\"journal\":{\"name\":\"Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003\",\"volume\":\"31 1\",\"pages\":\"0\"},\"PeriodicalIF\":0.0000,\"publicationDate\":\"2003-08-11\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"7\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003\",\"FirstCategoryId\":\"1085\",\"ListUrlMain\":\"https://doi.org/10.1109/CSB.2003.1227406\",\"RegionNum\":0,\"RegionCategory\":null,\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"\",\"JCRName\":\"\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.1109/CSB.2003.1227406","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"","JCRName":"","Score":null,"Total":0}
CoMRI: a compressed multiresolution index structure for sequence similarity queries
In this paper, we present CoMRI, compressed multiresolution index, our system for fast sequence similarity search in DNA sequence databases. We employ virtual bounding rectangle (VBR) concept to build a compressed, grid style index structure. An advantage of grid format over trees is subsequence location information is given by the order of corresponding VBR in the VBR list. Taking advantage of VBRs, our index structure fits into a reasonable size of memory easily. Together with a new optimized multiresolution search algorithm, the query speed is improved significantly. Extensive performance evaluations on human chromosome sequence data show that VBRs save 80%-93% index storage size compared to MBRs (minimum bounding rectangles) and new search algorithm prunes almost all unnecessary VBRs which guarantees efficient disk I/O and CPU cost. According to the results of our experiments, the performance of CoMRI is at least 100 times faster than MRS which is another grid index structure introduced very recently.