用移码延伸罚分法进行蛋白质编码序列的比对
Alignment of protein-coding sequences with frameshift extension penalties
摘要：
我们介绍了一种算法的比对蛋白质编码序列占移码。该算法的主要特点相比，以前发表的蛋白质编码序列比对方法是引入了一个罚成本移码延伸。以前的算法只使用恒定的移码惩罚关系。这类似于在经典序列比对算法中使用具有仿射空位罚分的评分方案。然而，比对中移码部分的总体罚分不能用仿射函数表示，因为它还应该包含不同的密码子取代评分。该算法的第二个特点是其搜索空间是在两个DNA序列之间的比对的经典定义下的两个编码序列之间的所有可能比对的集合。以前的算法已经引入了对路线长度的约束，以及用于表示路线中移码开口的附加符号。该算法具有与经典的Needleman-Wunsch算法相同的渐近空间复杂度和时间复杂度。
英文摘要：
We introduce an algorithm for the alignment of protein- coding sequences accounting for frameshifts. The main specificity of this algorithm as compared to previously published protein-coding sequence alignment methods is the introduction of a penalty cost for frameshift ex- tensions. Previous algorithms have only used constant frameshift penal- ties. This is similar to the use of scoring schemes with affine gap penalties in classical sequence alignment algorithms. However, the overall penalty of a frameshift portion in an alignment cannot be formulated as an affine function, because it should also incorporate varying codon substitution scores. The second specificity of the algorithm is its search space being the set of all possible alignments between two coding sequences, under the classical definition of an alignment between two DNA sequences. Previous algorithms have introduced constraints on the length of the alignments, and additional symbols for the representation of frameshift openings in an alignment. The algorithm has the same asymptotic space and time complexity as the classical Needleman-Wunsch algorithm.
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