摘要
Multiple sequence alignments with constraints are of priority concern in computational biology. Constrained sequence alignment incorporates the domain knowledge of biologists into sequence alignments such that the user-specified residues/segments are aligned together according to the alignment results. A series of constrained multiple sequence alignment tools have been developed in relevant literatures in the recent decade. GPU-REMuSiC is the most advanced method with the regular expression constraints, in which graphics processing units (GPUs) with CUDA are used. GPU-REMuSiC can achieve a speedup ratio of 29x for overall computation time based on the experimental results. However, the execution environment of GPU-REMuSiC must be constructed; it is a threshold for biologists to set up it. Therefore, this work presents an intuitive friendly user interface of GPU-REMuSiC for the potential cloud server with GPUs, called Cloud GPU-REMuSiC. Implementing the user interface via a network allows us to transmit the input data to a remote server without a complex cumbersome setting in a local host. Finally, the alignment results can be obtained from a remote cloud server with GPUs. Cloud GPU-REMuSiC is highly promising as an online application that is accessible without time or location constraints. Copyright © 2013, IGI Global.