Java与生物信息学：基因组数据分析与生物序列比对的科学之旅

    <!-- Maven依赖示例 -->
    <dependency>
    <groupId>org.biojava</groupId>
    <artifactId>biojava-core</artifactId>
    <version>5.2.0</version>
    </dependency>

    import org.biojava.nbio.core.sequence.DNASequence;
    import org.biojava.nbio.core.sequence.io.FastaReader;
    
    FastaReader reader = new FastaReader("sequence.fasta");
    for (DNASequence seq : reader.process()) {
    System.out.println("Sequence ID: " + seq.getAccession());
    System.out.println("Sequence Data: " + seq.getSequenceAsString());
    }

    import org.biojava.nbio.alignment.template.BlastProgram;
    import org.biojava.nbio.alignment.template.BlastTool;
    
    BlastTool blast = new BlastTool();
    blast.setProgram(BlastProgram.BLASTN);
    blast.setDatabase("path/to/your/database");
    blast.setSequence(seq1, seq2);
    Alignments alignments = blast.run();

    // 示例：使用伪代码表示ORF寻找过程
    for (int i = 0; i < dnaSequence.length() - 2; i++) {
    if (isStartCodon(dnaSequence.subSequence(i))) {
        int stopCodonPosition = findStopCodon(dnaSequence, i);
        if (stopCodonPosition != -1) {
            Gene gene = new Gene(dnaSequence.subSequence(i, stopCodonPosition));
            // 处理基因
        }
    }
    }

    import org.jfree.chart.ChartFactory;
    import org.jfree.chart.ChartPanel;
    import org.jfree.chart.JFreeChart;
    import org.jfree.data.category.DefaultCategoryDataset;
    
    DefaultCategoryDataset dataset = new DefaultCategoryDataset();
    dataset.addValue(value, "Alignment Score", "Sequence 1 vs Sequence 2");
    JFreeChart chart = ChartFactory.createBarChart("Alignment Scores", "Sequences", "Score", dataset);
    ChartPanel chartPanel = new ChartPanel(chart);

    // 示例：使用MySQL存储结果
    String query = "INSERT INTO results (sequence_id, alignment_score) VALUES (?, ?)";
    PreparedStatement statement = connection.prepareStatement(query);
    statement.setString(1, seq.getAccession());
    statement.setDouble(2, alignmentScore);
    statement.executeUpdate();

    // 示例：使用并行流处理生物序列数据
    List<DNASequence> sequences.parallelStream().forEach(this::processSequence);