EMMA: an efficient massive mapping algorithm using improved approximate mapping filtering.
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.
Zhang
Xin
X
Institute of Micro/Nano Science and Technology, Shanghai Jiaotong University, Shanghai 200030, China.
Cao
Zhi-Wei
ZW
Lin
Zhi-Xin
ZX
Wang
Qing-Kang
QK
Li
Yi-Xue
YX
D000465:Algorithms; D002874:Chromosome Mapping / Q000379:methods*; D019295:Computational Biology / Q000379:methods*; D018076:DNA, Complementary / Q000378:metabolism; D030541:Databases, Genetic; D015233:Models, Statistical; D010363:Pattern Recognition, Automated; D011381:Programming Languages; D015203:Reproducibility of Results; D012984:Software
D018076:DNA, Complementary