EMMA:An Efficient Massive Mapping Algorithm Using Improved Approximate Mapping Filtering  

作　　者：Xin ZHANG Zhi-Wei CAO Zhi-Xin LIN Qing-Kang WANG Yi-Xue LI 

机构地区：[1]Institute of Micro/Nano Science and Technology, Shanghai Jiaotong University, Shanghai 200030, China [2]Shanghai Center for Bioinformation Technology, Shanghai 200235, China [3]College of Life Science and Technology, Shanghai Jiaotong University, Shanghai 200030, China [4]Bioinformation Center of Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China

出　　处：《Acta Biochimica et Biophysica Sinica》2006年第12期857-864,共8页生物化学与生物物理学报（英文版）

基　　金：This work was supported by a grant from the Major State Basic Research Development Program of China (No.2004CB720103)

摘　　要：Efficient massive mapping algorithm （EMMA）, an algorithm on efficiently mapping massive cDNAs onto genomic sequences, has recently been developed. The process of mapping massive cDNAs onto genomic sequences has been improved using more approximate mapping filtering based on an enhanced suffix array coupled with a pruned fast hash table, algorithms of block alignment extensions, and k-longest paths. When compared with the classical BLAT software in this field, the computing of EMMA ranges from two to forty-one times faster under similar prediction precisions.Efficient massive mapping algorithm （EMMA）, an algorithm on efficiently mapping massive cDNAs onto genomic sequences, has recently been developed. The process of mapping massive cDNAs onto genomic sequences has been improved using more approximate mapping filtering based on an enhanced suffix array coupled with a pruned fast hash table, algorithms of block alignment extensions, and k-longest paths. When compared with the classical BLAT software in this field, the computing of EMMA ranges from two to forty-one times faster under similar prediction precisions.

关 键 词：cDNA mapping maximal exact match enhanced suffix array pruned fast hash table extension algorithm 

分 类 号：Q753[生物学—分子生物学]