Sequence alignment

Why do we need sequence matching ？ What is the difference between similarity and homology ？

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2021-05-05 16:54

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The basic premise of constructing phylogenetic tree is that the sequences used must be homologous .

1.  Sequence coupling （Alignment） Purpose ：

All tree building methods assume that all bases in any column of a group of homologous sequences are homologous （ That is, they all originated from the same base in the ancestral sequence ）. Without insertion and mutation （ Collectively referred to as ：indels）, Then the two sequences are the same length , And every base is homologous matching from beginning to end .

But in fact, insertional deletion does exist , This will change the sequence length , Move the position of the base , And will affect the sequence of amino acids . However , Sequence alignment （Alignment） Is the process of introducing gaps in the sequence , The purpose is to move bases to their corresponding homologous positions . This process is very important , Determines the quality of the phylogenetic tree constructed .

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2.  The difference between homology and similarity （ It's very important ）：

In the process of constructing phylogenetic tree, we must distinguish homology and similarity .

“ Homology ” It means that two groups or sequences are descendants of the same ancestor , In sequence coupling （Alignment） The same base at homologous sites is caused by genetic relationship .

However ,“ similarity ” It only reflects that the trait status of some loci is the same . For example, two non homologous sequences can also be combined , Some parts of the base will be exactly the same （ This is why we are online blast When the gene sequence in your hand , Some other genes with high matching degree often appear in the results ）, But the same base is not the result of inheritance from the same ancestor .

obviously , No matter how similar the two sequences are , It is meaningless to put two non homologous sequences on the same tree （ Because the purpose of establishing trees is to show the genetic evolution process from a common ancestor ）.

at present , In some published papers, phylogenetic trees containing non homologous sequences also appear , For example, a group of proteases have similar catalytic properties and reaction mechanism , It is not uncommon to be given the same name , Then they will be placed in the same system tree , Regardless of whether it is homologous or not .