Constructing Multiple Sequence Alignments - Exercise Week 9

ClustalW is a very popular software program to build multiple sequence alignments. ClustalW is available over many web-interfaces. One of them can be found at: http://www.ch.embnet.org/software/ClustalW.html. You can pass the sequences to ClustalW in the so-called Fasta format. Within this format each sequence has a description line starting with  > and the sequence starts on the next line and is all subsequent lines until the next line that starts with a > indicating that a new sequence starts. For more information on the Fasta format, see: http://www.ch.embnet.org/software/ClustalW_help.html

A newer and much faster MSA program is Mafft, also available as a web service.

Darwin has also some implemented algorithms to construct MSAs. These algorithms are implemented in the Darwin procedure called MAlign.  See ?MAlign and ?MAlignment for help. The result from MAlign is a MAlignment data structure. Create a multiple sequence alignment with the 'prob' method.  Using print will pretty print the alignment, the optimal score and the pairwise scores.

Task

Use the Triosephosphate Isomerase sequences from Human, Monkey, Mosquito and Rice (or any set of homologous sequences of your choice) and build a multiple sequence alignment with ClustalW, Mafft and Darwin's MAlign algorithm. The accession numbers (AC) of those sequences in SwissProt are:

Compare the alignments with respect to where they placed the gaps. Let us assume that you want to use these MSA's to do protein structure prediction. Would you predict similar or different structures based on the MSA's from the different methods?