Author(s)

Shuaibin Lian^*, Tianliang Liu, Ke Gong, Xinwu Chen, Gang Zheng

School of Physics and Electronic Engineering, Xinyang Normal University, Xinyang City, China.

Eukaryotic genomes contain a significant fraction of repeats, which have very important biomedical function. Thus, aligning repeats from short sequences back to reference genome is the key step for further genome analysis. Unfortunately, the current aligning algorithms performed poorly in distinguishing repeats and nonrepeats. To this end, we proposed a new algorithm, named HashRepAligner, to address this problem. Finally, the cross comparison with other algorithms was performed, and the results indicated that HashRepAligner outperformed other aligners in terms of the detecting repeats.

Sequence Alignment, Next Generation Sequencing, Hash Index, Repeats Detection

Lian, S. , Liu, T. , Gong, K. , Chen, X. and Zheng, G. (2016) A Complete and Accurate Short Sequence Alignment Algorithm for Repeats. Journal of Biosciences and Medicines, 4, 144-151. doi: 10.4236/jbm.2016.412018.