In bioinformatics, a protein sequence comparison between two banks is one of most important algorithms. The sequence bank size is becoming larger and larger with the development of biotechnology, while the algorithm is also computation intensive. This leads to more and more consumption time and the single processor or multicore system, with only a few cores, are not powerful enough to reach a satisfying speed nowadays. Godson-T is a new kind of many-core architecture with lots of novel features. The parallelization of a protein sequence comparison algorithm on Godson-T is implemented. At the same time, the algorithm structure and architecture features of Godson-T are combined, and some optimization in three aspects are made: synchronization overhead, memory access contention, and load balance. The result shows that a close to linear speedup is obtained, and the performance is much better than that of the workstation platform based on the AMD Opteron processor.