A NEW APPROACH FOR ALIGNMENT OF MULTIPLE PROTEINS

摘要

We introduce a new graph-based multiple sequence alignment method for protein sequences. We name our method HAS (Horizontal Sequence Alignment) for it horizontally slides a window on the protein sequences simultaneously. Current progressive alignment tools build up final alignment by adding sequences one by one to existing alignment. Thus, they have the shortcoming of order-dependent alignment. In contrast, HAS considers all the proteins at once. It obtains final alignment by concatenating cliques of graph. In order to find a biologically relevant alignment, HAS takes secondary structure information as well as amino acid sequences into account. The experimental results show that HAS achieves higher accuracy compared to existing tools on BAliBASE benchmarks. The improvement is more significant for proteins with low similarity.