Python Programming for Biology: Bioinformatics and Beyond

Alignment consensus and profiles

Before we begin to look at routines to generate multiple alignments we will look at some

routines to analyse multiple alignments, given that this will be useful in their construction.

Firstly,  we  will  consider  the  consensus  of  a  sequence  alignment.  This  means  the

compression  of  multiple  aligned  sequences  into  one  representative  or  average  sequence.

This  will  typically  be  a  completely  unnatural  sequence,  but  it  will  have  many  of  the

overall  properties  of  the  alignment.  Consider  the  following  multiple  alignment,  with  the

consensus line below. You can see that the residues in the consensus sequence are simply

formed by taking a poll of the most popular residue type at each position. Note that in this

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particular  example  we  have  not  considered  gaps;  a  residue  letter  always  wins  out  over  a

dash, but this needn’t always be the case.

Seq1: SRPAPVVIILIILCVMAGVIGTILLISYGIRLLIK

Seq2: TVPAPVVIILIILCVMAGIIGTILLISYTIRRLIK

Seq3: HHFSEPEITLIIFGVMAGVIGTILLISYGIRRLIK

Seq4: HEFSELVIALIIFGVMAGVIGTILFISYGSRRLIK

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Cons: HVPSPVVIILIILGVMAGVIGTILLISYGIRRLIK