clustal omega.pptx

Clustal omega is a widely used bioinformatics tool for performing multiple sequence alignment. This ppt contains the concept and types of sequence alignment, algorithms followed by clustal omega, its result interpretation and applications.

1. CLUSTAL OMEGA (MULTIPLE SEQUENCE ALIGNMENT) AINDRILA MITRA BBT4

2. Sequence alignment: A sequence alignment is a way of arranging sequences of DNA , RNA or protein to identify regions of similarity that may be consequence of functional, structural or evolutionary relationships between the sequence. In sequence alignment- The known sequence is known as the reference sequence. The unknown sequence is known as the query sequence. 1

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4. Pairwise sequence alignment: It is used to align two biological sequence only. Methods of primary sequence alignment: 1.Dynamic Programming: It is a general algorithm for solving certain optimization problem. This technique can be applied to produce- > Global alignment (Needleman-Wunsch algorithm) > Local alignment (Smith-Waterman algorithm) 2.Dot Matrix: It is a grid system where the similar nucleotides of two DNA sequences are represented as dots. 3

5. Multiple sequence alignment: Multiple sequence alignment (MSA) is generally the alignment of three or more biological sequence of similar length. MSAs are often used in identifying conserved sequence regions across a group of sequences hypothesized to be evolutionarily related. Alignments are also used to aid in establishing the evolutionary relationship by constructing phylogenetic tree. 4

6. APPLICATION OF MSA : Detection of structural homologies. Detection of conserved domains. Construction of phylogenetic tree. Prediction of a protein structure. Determination of a consensus sequence. 5

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8. Dynamic Programming Progressive Method Iterative Method Motif Finding Hidden Markov Model(HMM) This is an extension of dynamic programming approach for pairwise alignment to multiple sequence. Because of its high running time it is not typically used in practice. Progressive , hierarchical, or tree methods generate a multiple sequence alignment by first aligning the most similar sequence and then adding successively less related sequences or groups to the alignment until the entire query set has been incorporated into the solutions It is a method of performing a series of steps to produce successively better approximation to align many sequence step-by-step. Here the pairwise sequence alignment is totally avoided. It is also known as profile analysis, constructs global multiple sequence alignments that attempt to align short conserved sequence in the query set. Hidden Markov model have been used to produce probability scores for a family of possible multiple sequence alignments for a given query set. 7

9. MSA TOOLS 8

10. https://www.researchgate.net/publication/275954941_Multiple_Sequence_Alignment_Tools_Assessing_Performance_of_the_Underlying_Algorithms LIST OF MSA TOOLS: 9

11. CLUSTAL OMEGA : (https://www.ebi.ac.uk/Tools/msa/clustalo/) The Clustal series of programs are widely used in molecular biology for the multiple alignment of both nucleic acid and protein sequences and for preparing phylogenetic tree. Example: Clustal V, Clustal W, Clustal X, Clustal omega, Clustal2 Clustal omega has the widest variety of operating systems out of all the clustal tools. 10

12. Clustal omega uses seeded guide tree and HMM profile-profile techniques to generate alignment. Clustal omega follows 5 main steps: 1. The first is producing a pairwise alignment using the k-tuple method, also known as the word method. 2. After that the sequence are clustered using the modified mBed method. 3. It is followed by the k- means clustering method. 4. Guide tree is constructed using UPGMA algorithm. 5. In the final step, the multiple sequence alignment is produced using HHAlign package from the HH-Suite which uses two profile HMM. Fig: Flowchart of algorithms used in clustal omega ( https://en.wikipedia.org/wiki/Clustal#/media/File:Clustal_Omega_Algorithm_Flowchart.svg ) 11

13. STEPS : Step1: go to NCBI> select gene>search 12

14. Step2: select Homo sapiens> redirect to new page 13

15. Step3: select genbank > new page>scroll down> cds > protein id>click 14

16. Step4: select run BLAST 15

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18. Step5: select organism based on percentage identity> download the FASTA (aligned sequence) 17

19. Step6: go to Clustal omega> paste the sequence>submit 18

20. Conservative mutation(:) Conserved sequence (*) Gap(-) Semi conservative mutation(.) 19 Interpretation of the Sequence alignment:

21. Conserved sequence(*): t he amino acid is the same for all sequences at that position . Conservative substitution(:) : The replacement of an amino acid residue in one protein by one with similar chemical properties in another protein . Non-conservative substitution(): The replacement of an amino acid residue in one protein by one with dissimilar chemical properties in another protein. Semi-conservative substitution(.):  which is somewhere between a conservative and nonconservative substitution. This means that the chemical properties of the amino acids at that position are similar, but not that similar. 20

22. Different colours represents different amino acid residues according to their physicochemical properties. https://www.ebi.ac.uk/seqdb/confluence/display/JDSAT/Clustal+Omega+FAQ 21

23. Phylogenetic tree is a branching diagram showing the evolutionary relationships among the given sequences. Cladogram is a type of phylogenetic tree which only represent the branching pattern. 22

24. Conclusion: Clustal omega uses a modified iterative progressive alignment method and can align over 10,000 sequences quickly and accurately. It is very useful for finding evidence of conserved function in DNA and protein sequences. 23

25. REFERENCE: https://www.researchgate.net/publication/10693451_Multiple_sequence_alignment_with_the_CLUSTAL_series_of_programs https://pubmed.ncbi.nlm.nih.gov/33289883/ https://en.wikipedia.org/wiki/Clustal https://www.slideshare.net/ShumailaRiaz6/multiple-alignment-sequence-using-clustal-omega-shumaila-riaz https://www.ebi.ac.uk/seqdb/confluence/display/JDSAT/Clustal+Omega+FAQ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9024764/ https://www.slideshare.net/MariyaRaju/multiple-sequence-alignment-76802660 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5734385/ https://www.researchgate.net/publication/275954941_Multiple_Sequence_Alignment_Tools_Assessing_Performance_of_the_Underlying_Algorithms

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