Java与生物信息学：基因序列比对算法

    public class NeedlemanWunsch {
    public static int[][] align(String seq1, String seq2) {
        int m = seq1.length();
        int n = seq2.length();
        int[][] score = new int[m + 1][n + 1];
    
        // 初始化边界条件
        for (int i = 0; i <= m; i++) {
            score[i][0] = -i * gapPenalty;
        }
        for (int j = 0; j <= n; j++) {
            score[0][j] = -j * gapPenalty;
        }
    
        // 填充评分矩阵
        for (int i = 1; i <= m; i++) {
            for (int j = 1; j <= n; j++) {
                int match = score[i - 1][j - 1] + (seq1.charAt(i - 1) == seq2.charAt(j - 1) ? 1 : -1);
                int delete = score[i - 1][j] - gapPenalty;
                int insert = score[i][j - 1] - gapPenalty;
                score[i][j] = Math.max(match, Math.max(delete, insert));
            }
        }
    
        // 回溯找到比对结果
        // ...
    
        return score;
    }
    
    // 定义间隙惩罚分数
    private static final int gapPenalty = 1;
    
    public static void main(String[] args) {
        String sequence1 = "ACGT";
        String sequence2 = "AGCT";
    
        int[][] alignmentScore = align(sequence1, sequence2);
        // 打印评分矩阵或比对结果
    }
    }