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has been cited by the following article:

• TITLE: A Complete and Accurate Short Sequence Alignment Algorithm for Repeats

  AUTHORS: Shuaibin Lian, Tianliang Liu, Ke Gong, Xinwu Chen, Gang Zheng

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

  JOURNAL NAME: Journal of Biosciences and Medicines, Vol.4 No.12, December 14, 2016

  ABSTRACT: 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.