With the improvement of biological techniques, the amount of biosequences data, such as DNA, RNA and protein sequences, are growing explosively. It is almost impossible to handle such huge amount of data purely by manpower. Thus the requirement of the great computing power is essential. There are some ways to treat biosequence data, finding identical biosequences, searching similar biosequences, or mining the signature of biosequences. All of these are based on the same problems, the biosequence alignment problems. In this dissertation, we shall study the biosequence alignment problems to raise the biological meaning of the optimal or near-optimal alignments since the biologists and computer scientists sometimes argue the biological meaning of the mathematically optimal alignment obtained based on some scoring functions. We first study the methods to improve the optimal alignment of two given biosequences. Since usually the optimal alignment is not unique, there should exist the best one among the optimal alignments, and we try to extract this by defining some other criteria to judge the goodness of the alignments when the traditional methods cannot decide which is the better one. Two algorithms are proposed for solving the newly defined biosequence alignment problems, the smoothest optimal alignment and the most conserved optimal alignment problems. Some other criteria are also discussed since most of them can be solved in a similar way. Then we notice that the most biologically meaningful alignment may not be the optimal one since there is no perfect scoring matrix. We address our candidates in those near-optimal alignments, and present a tracing marking function to get all near-optimal alignments and use the criterion "the most conserved" to filter it, which is named as the near-optimal block alignment (NBA) problem. Finally, as everybody knows that existing scoring matrices are not perfect at all, we try to figure out how we choose the winner when multiple scoring matrices are applied. We define some reasonable schemes to decide the winner alignment. In this dissertation, we solve and discuss the algorithms for near-optimal alignment problems on biosequences. In the future, we would like to do some experiments to support or reject these concepts.