Python Programming for Biology: Bioinformatics and Beyond

Interfacing multiple-alignment programs

The above examples show you the basic mechanisms of how multiple alignments can be

made.  However,  unless  you  wish  to  develop  your  own  routines,  when  doing  multiple

alignments  in  most  laboratory  situations  the  best  solution  is  to  use  existing,  tried,  tested

and  documented  programs.  Common  programs  like  ClustalW,

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 MUSCLE

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 or  T-Coffee

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are  easily  interfaced  with  other  routines  by  using  Python  to  write  input  files  and  read

output files. With experience you could write your own functions to achieve this; however,

if  you  are  using  common  file  formats  then  it  is  easiest,  and  safer,  to  use  the  BioPython

modules. The following example shows how you can make input for, execute and read the

output  of  ClustalW.  ClustalW  is  arguably  the  most  widely  known  multiple-alignment

program, and one that offers a good compromise between speed and accuracy. Using the

same principles you can easily adapt the approach to use other programs.

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