HMMER
基于隐马尔可夫模型的序列分析算法，使用概率模型检测远程同源序列和蛋白质结构域。 该方法比简单的序列比对更敏感，能够发现进化距离较远的同源关系。
| Property | Value |
|---|---|
| Purpose | 蛋白质结构域识别和远程同源检测 |
| Time Complexity | O(mn) |
| Space Complexity | O(m) |
| Year | 2011 |
| Category | Functional Annotation |
Complexity Analysis
- Time Complexity:
O(mn) - Space Complexity:
O(m)
Performance Insight: The time complexity of this algorithm is quadratic matrix (O(mn)), SIMD acceleration or approximate methods are advised when m, n exceed 10⁴.
Note: Complexity analysis is based on theoretical models. Actual runtime is affected by input scale, hardware, and implementation optimizations. Benchmark for your specific workload.
Literature & Implementation
Related Tools
Pfam · InterProScan · SMART