Python Programming for Biology: Bioinformatics and Beyond

Generating simple multiple alignments in Python

With a function that can align profiles, we can now consider building multiple alignments.

Ideally, as previously mentioned you would make a genetic tree of the sequences and join

them into a multiple alignment in the same manner as the tree branches. However, because

we’ll leave tree generation until later, we will only do a crude multiple-sequence assembly

and add sequences one at a time to a growing multiple alignment, which will be enough to

illustrate the procedure. Because sequence alignment works with a pair of inputs, we will

have  a  pair  of  profiles  that  are  to  be  aligned,  each  (potentially)  representing  smaller

alignments  that  have  already  been  combined.  Repeating  this  procedure  the  multiple

alignment grows, in terms of the number of sequences, as more profiles are added. Note

that it would also be possible to generate multiple alignments using consensus sequences,

rather  than  profiles.  A  function  to  do  this,  consensusMultipleAlign,  is  given  in  the

downloadable

material

that

accompanies

this

book

(

http://www.cambridge.org/pythonforbiology

). You will note that because a consensus is a

regular  sequence  representation  only  regular  sequence  alignment  is  required  within  the

function, rather than having to do profile alignments.