Method and computer program product for aligning similarity of two biological sequences

摘要

The present invention provides a method and a computer program product for similarity alignment of two biological sequences, such as nucleotide sequences and amino acid sequences. First of all, a seed pair in two biological sequences is selected by satisfying a user-defined limitation. Two fragments are extended in the same direction. If the data arrangement between the two extended fragments satisfies an extension condition, two other fragments are further extended subsequently. Otherwise, it is then to match the fragments by gap insertion. After gap insertion, if the data arrangement becomes to satisfy the extension condition, then two fragments start to be extended. Otherwise the extension is terminated and resulted fragments are obtained.