Multiple Sequence Alignment

PPT on the given topic "Multiple Sequence Alignment".

1. Birla Institute Of Technology, Mesra Jaipur Presented By Anushka Pareek MCA/25024/18 Topic :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. In many cases, the input set of query sequences are assumed to have an evolutionary relationship. By which they share a lineage and are descended from a common ancestor. From the output, homology can be inferred and the evolutionary relationship between the sequence studied.

3. Purpose of MSA In order to characterize protein families ,identify shared regions of homology in a multiple sequence alignment. Determination of the consensus sequence of several aligned sequences. Consensus sequence scan help to develop a sequence “fingerprint” which allows the identification of members of distantly related protein family (motifs). MSA can help us to reveal biological facts about proteins, like analysis of the secondary/tertiary structure.

4. Types Of MSA Dynamic Programming approach Progressive method Iterative method

5. 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.

6. Dynamic Programming

7. 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 then less 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

8. Progressive Alignment – Step 1 Steps in Multiple Alignment Pairwise Alignment

9. Progressive Alignment – Step 2 Multiple Alignment following the tree from A.

10. Pros of Progressive Alignment Efficient enough to implement on a large scale for many (100s to 1000s) sequences. Progressive alignment services are commonly available on publicly accessible web servers, so users need not locally install the applications of interest. Most widely used method of multiple sequence alignment because of speed and accuracy.

11. 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.

12. Steps In Iterative Method

13. Tools Involved in MSA Clustal W Clustal W2 Clustal Omega MAFFT MUSCLE M View T-Coffee Web PRANK MACAW

14. 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.

15. Thank You