Java Bioinformatics - 获取字符串中多个特定单词的所有索引

Question

我在大学的生物信息学类(class)中有一个项目，我项目中的其中一件事是基因预测。

我今天的问题是如何获取字符串中多个特定单词的所有索引。例如，在我这里的例子中，我想找到所有出现的起始密码子 ("AUG") 和终止密码子 ("UAA","UAG", "UGA") 并使用它们来预测基因，只需尝试做 开放阅读框 (ORF)

这是我的初始代码:

private void jButton3ActionPerformed(java.awt.event.ActionEvent evt) {                                         
    // TODO add your handling code here:
    //   textArea1.setText(null);\
    String str = jTextField1.getText(), y = "", gene = "", dnax = "", text = "";
    SymbolList dna = null;
    int start_codon_index = -1, stop_codon_index = -1;
if ("".equals(str)) {
    jTextArea1.setText("No DNA strand entered.. ");

} else {
    if (checksum(str) == 100) {
        try {
            dna = DNATools.createDNA(str);
        } catch (IllegalSymbolException ex) {
            Logger.getLogger(m.class.getName()).log(Level.SEVERE, null, ex);
        }
        try {
            dna = DNATools.toRNA(dna);
        } catch (IllegalAlphabetException ex) {
            Logger.getLogger(m.class.getName()).log(Level.SEVERE, null, ex);
        }
        dnax = dna.seqString().toUpperCase();
        if (dnax.length() % 3 != 0) {
            if (dnax.length() % 3 == 1) {
                dnax += "-";
            }
            if (dnax.length() % 3 == 2) {
                dnax += "-";
            }
        }
        //  System.out.println(dnax);
        for (int g = 0; g < dnax.length(); g += 3) {
            y = dnax.substring(g, g + 3);
            if ("AUG".equals(y)) {
                start_codon_index = g;
            } else if (start_codon_index != -1 && ("UGA".equals(y) || "UAG".equals(y) || "UAA".equals(y))) {

                stop_codon_index = g + 3;

            }
        }

        if (stop_codon_index != -1 && start_codon_index != -1) {
            String k = "";
            int a = 0;
            for (a = start_codon_index; a < stop_codon_index; a++) {
                gene += dnax.charAt(a);

            }
            text += "\nGene start position:  " + start_codon_index + "\nGene end position:  " + a + "\n Gene: " + gene;
            jTextArea1.setText(text);

        } else {

            jTextArea1.setText("No genes found in Seq: " + dnax);

        }
    } else {
        jTextArea1.setText("Text entered is not a DNA strand..");
    }
}
}

这里是 checksum() 方法:

private static int checksum(String x) {
    int i = 0, checks = 0, count = 0;
    char c;
    x = x.toUpperCase();
    while (i < x.length()) {
        c = x.charAt(i);
        if (c == 'A' || c == 'T' || c == 'G' || c == 'C' || c == '-') {



    count++;
    }
    i++;
}
try {
    checks = (count / x.length()) * 100;
} catch (Exception e) {
    e.printStackTrace();
}

return checks;
}

我尝试过其他解决方案，但对我来说没有任何效果。欢迎任何帮助/建议。

Answer 1

我想你是在问如何找到那些特定密码子的索引？ dnax 是您要检查的字符串吗？

您可以使用 indexOf(String str, int fromIndex)。如果未找到子字符串，则返回 -1。

所以也许这样的事情可能会有所帮助，

List<Integer> startCodonIndices = new ArrayList<Integer>();
int index;
for (int i=0; i+3<dnax.length(); i++) {
    index = indexOf("AUG", i);
    startCodonIndices.add(index);
}