二，序列比对的类型
2.1 Pairwise Sequence Alignment (PSA) is used to identify regions of similarity that may indicate functional, structural and/or evolutionary relationships between two biological sequences (protein or nucleic acid).
https://www.ebi.ac.uk/seqdb/confluence/display/JDSAT/Pairwise+Sequence+Alignment
两两比对又分为下面几种类型

全局比对试图对齐整个序列，比较适合相似度高而且长度比较类似的序列。
局部比对试图找出来局部连续的子序列，序列长度不同，序列有共同特征时，比较适合这种方式。

两两比对有如下几种方法：

1. Dot matrix analysis
   除非序列非常相似，都应该首先使用该方法。因为该方法可以展示所有的对齐可能，包括插入、删除、重复等。
   

https://www.sanger.ac.uk/tool/seqtools/
seqtools里面有一个叫dotter的工具　可以查看dot矩阵图
2. The dynamic programming (or DP) algorithm
比较费内存　但是很适合找最优对齐
3. Word or k-tuple methods, such as used by the programs FASTA and BLAST
比较适合搜索大型数据库

2.2 Multiple Sequence Alignment (MSA) is generally the alignment of three or more biological sequences (protein or nucleic acid) of similar length. From the output, homology can be inferred and the evolutionary relationships between the sequences studied.

By contrast, Pairwise Sequence Alignment tools are used to identify regions of similarity that may indicate functional, structural and/or evolutionary relationships between two biological sequences.https://www.ebi.ac.uk/seqdb/confluence/display/JDSAT/Multiple+Sequence+Alignment

https://www.semanticscholar.org/paper/Comparative-Analysis-of-Multiple-Sequence-Alignment-Mohamed-Mousa/c8c60c0708d1953196f6a558bab896c6e0ec9a1e

三，序列比对的应用
3.1　物种分类
https://help.ezbiocloud.net/pairwise-nucleotide-sequence-alignment/

距离评价(distance score):
mismatches/(matches+mismatches)
3.2 overlap determination in genome sequence assembly[4]
3.3 gene finding and comparison[4]
3.4 protein sequence comparison[4]

参考资料：
1.Bioinformatics: Sequence and Genome Analysis
2.https://www.ebi.ac.uk/seqdb/confluence/display/JDSAT/Pairwise+Sequence+Alignment
3.https://www.codeproject.com/Articles/304772/DNA-Sequence-Alignment-using-Dynamic-Programming-A
4.Reducing storage requirements for biological sequence comparison
https://github.com/Peteraya/fer_bioinformatics