,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: Institute of Micro/Nano Science and Technology, Shanghai Jiaotong University, Shanghai 200030, China
• 出 处: 生物化学与生物物理学报（英文版）
• 发表日期: 2006年12期
• 关键词: cDNA mapping maximal exact match enhanced suffix array pruned fast hash table ex

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.