Multiple sequence alignment

Exercises

1. What's the SP-score of the following row in a multipe alignment?
   (assume PAM250-similarity (K,R) = 3 and gapcost=(-12))

   			
   			R
   			-
   			K
   

2. Which program allocates more memory, Clustal or MSA?
   theory
   
   
3. Here is a list of Web-Sites containing tools for Multiple-Sequence-Alignments.
   
   
   • Integration of Multiple Alignment and Phylogenetic Tree Construction
     
     
     theory
     
     
   • Divide-and-Conquer Multiple Sequence Alignment (at bibiserv.techfak.uni-bielefeld.de)
     
     
     Introduction
     
     
     SP-optimal MSA
     
     
   • ctre, ClustalW, MSA
     
     
     theory
     
     
   • DIALIGN 2
     
     
     theory
     
     
   
   The first link in the list is the MSA-page of our Web-Server at TBI,
   which also provides a visualization of the corresponding Phylogenetic Trees.
   
   BAliBASE is a database containing (biologically) correct multiple alignments for benchmark tests
   and the evaluation of multiple sequence alignment programs.
   
   Take the sequences of BAliBASE and align them using different programs.
   Judge and compare the results.