We introduce a new graph-based multiple sequence alignment method for protein sequences. We name our method HSA (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, HSA considers all the proteins at once. It obtains final alignment by concatenating cliques of graph. In order to find a biologically relevant alignment, HSA takes secondary structure information as well as amino acid sequences into account. The experimental results show that HSA achieves higher accuracy compared to existing tools on BAliBASE benchmarks. The improvement is more significant for proteins with low similarity.