评价指标

SP score

Sum of pairs (SP) score: Scoring a alignment based on pairwise alignments.

计算公式

$$SP\mathrm{\_}score(\alpha )=\sum _{i<j}score({\alpha }_{ij})$$

计算方式分为两种（注：p(-,-)=0）:

• 对多序列对齐中的每一列得分进行计算，最后相加
• 对多序列对齐中的每一对PSA得分进行计算，最后相加

参考内容

课题组工具 spscore 可计算已完成核酸多序列比对的 SP 得分，支持 FASTA 和 gzip 输入。安装、评分约定和输出说明见课题组软件中的 spscore 小节。

1. Altschul, Stephen F. "Gap costs for multiple sequence alignment." Journal of theoretical biology 138.3 (1989): 297-309.
2. SP 教学实现

Q score

Q (quality) score is the number of correctly aligned residue pairs divided by the number of residue pairs in the reference alignment. This has previously been termed the developer score and SPS.

计算公式

$Q=\frac{{\sum }_{k=0}^{L}q(k)}{{\sum }_{k=0}^{L}ref(k)}$

第k列：$q(k)=\frac{tes{t}_{match}\times (tes{t}_{match}-1)}{2}$ , $ref(k)=\frac{re{f}_{match}\times (re{f}_{match}-1)}{2}$

其中：

• $re{f}_{match}$是在ref文件的第𝑘列中大写碱基的个数
• $tes{t}_{match}$是在test文件的第𝑘列中可以和ref文件完全匹配的碱基个数（大写且相同）

参考内容

1. Edgar, Robert C. “MUSCLE: multiple sequence alignment with high accuracy and high throughput.” Nucleic acids research vol. 32,5 1792-7. 19 Mar. 2004, doi:10.1093/nar/gkh340
2. Sauder, J M et al. “Large-scale comparison of protein sequence alignment algorithms with structure alignments.” Proteins vol. 40,1 (2000): 6-22. doi:10.1002/(sici)1097-0134(20000701)40:1<6::aid-prot30>3.0.co;2-7
3. Thompson, J D et al. “A comprehensive comparison of multiple sequence alignment programs.” Nucleic acids research vol. 27,13 (1999): 2682-90. doi:10.1093/nar/27.13.2682
4. Q score源代码

TC score

Total column(TC) score is the number of correctly aligned columns divided by the number of columns in the reference alignment; this is Thompson et al.’s CS and is equivalent to Q in the case of two sequences (as in PREFAB).

计算公式

$TC=\frac{{\sum }_{k=0}^{L}match(tes{t}_k,ref)}{re{f}_{upper}}$

其中：

• $re{f}_{upper}$是ref文件中包含大写字母的列数
• $match(tes{t}_k,ref)$是在test文件中完全匹配(大写且相同)的列数

参考内容

1. Edgar, Robert C. “MUSCLE: multiple sequence alignment with high accuracy and high throughput.” Nucleic acids research vol. 32,5 1792-7. 19 Mar. 2004, doi:10.1093/nar/gkh340
2. Thompson, J D et al. “A comprehensive comparison of multiple sequence alignment programs.” Nucleic acids research vol. 27,13 (1999): 2682-90. doi:10.1093/nar/27.13.2682
3. TC score源代码