Duplicate removal algorithms of Indel Gap in protein sequence alignment

In this paper, a newly algorithm is proposed to deal with the Gap detection and duplicate removal problems in protein sequence alignment. After analysed the different causes of Gaps from the view of different points of mutations, there are two types of Gaps should be treated using different algorithms. The duplicate removal algorithms attempt to find all the duplicate Gaps is described with the feature of introduce a nested linked list in storing duplicate Gaps, which decrease the time complexity significantly. The software based on the algorithms have developed and used to treat the enormous Gap information from protein sequence alignment files in practices.