Multiple sequence alignment

It is sequence analysis tool

1. S.Ramya I M.Sc Microbiology Multiple Sequence Alignment

2. Multiple Sequence Alignment Multiple Sequence Alignment(MSA) is generally the alignment of three or more biological sequence (Protein or Nucleic acid) of similar length . From the output, homology can be inferred and the evolutionary relationship between the sequence studied .

3. Types of MSA Dynamic Programming approach Progressive method Iterative method

4. Dynamic Programming Approach In fact, dynamic programming is applicable to align any number of sequences. Computes an optimal alignment for a given score function. Because of its high running time, it is not typically used in practice.

5. Dynamic Programming

6. Progressive Method In this method, pairwise global alignment is performed for all the possible and these pairs are aligned together on the basis of their similarity. The most similar sequences are aligned together and thenless related sequences are added to it progressively one-by-one until a complete multiple query set is obtained. This method is also called hierarchical method or tree method

7. Progressive alignment (Step 1)

8. Progressive alignment (Step 2)

9. Iterative Method A method of performing a series of steps to produce sucessively better approximation to align many sequences step-by-step is called iterative method. Here the pairwise sequence alignment is totally avoided. Iterative methods attempt to improve on the weak point of the progressive methods the heavy dependence on the accuracy of the initial pairwise alignment .

10. Steps in Iterative Method

11. Tools involved in MSA Clustal W Clustal W2 Clustal Omega Kalign MAFFT MUSCLE M View T-Coffee Web PRANK MEME MACAW

12. Applications of MSA Detecting similarities between sequences(closely or distinctly related). Detecting conserved regions or motifs in sequences. Detecting of structural homologies. Thus, assisting the improved prediction of secondary and tertiary structures of proteins.