Global and Local Sequence Alignment

Global and Local Sequence Alignment

1. Global and Local Sequence Alignment -Presented by Ajay Balasaheb Patil

2. O utline • Introduction • Principle • Types of alignment - global alignment local alignment Dot plot for sequence comparision Scoring Matrics • Dynamic programming method • BLAST and types of BLAST • References

3. Introduction A sequence alignment is a way of arranging the primary sequences of DNA , RNA, or protein to identify regions of similarity that may be a consequence of functional, structural, or evolutionary relationships between the sequences . The sequence alignment is made between a known ssequence and unknown sequence or between two unknown sequences . The known sequence is called reference sequence, unknown sequence is called query sequence .

4. P rinciple Alignment can reveal homology between sequences Similarity is descriptive term that tells about the degree of match between the two sequences Sequence similarity does not always imply a common function Conserved function does not always imply similarity at the sequence level Convergent evoluation ; sequences are highly similar, but are not homologous

5. Types of alignment Based on completeness, it was classified as three types. they are , (a ) Global alignment (b) Local alignment (c) semi global alignment

6. Global alignment Is the matching the residues of two sequences across their entire length. It matches the identical sequences . To align every residue in every sequence, are most useful when the sequences in the query set are similar and of roughly equal size . A general global alignment technique is called the Needleman – Wunch algorithm and is based on dynamic programming.

7. Local alignment Is a matching two sequence from regions which have more similar with each other. These are more useful for dissimilar sequences that are suspected to contain regions of similarity or similar sequence motifs within their larger sequence context. The Smith –Waterman algorithm is a general local alignment method also based on dynamic programming.

8. Interpreting dot plot-bioinformatics with an example In bioinformatics a dot plot is a graphical method that allows the comparison of two biological sequences and identify regions of close similarity between them. A dot plot is a simple, yet intuitive way of comparing two sequences, either DNA or protein, and is probably the oldest way of comparing two sequences.

9. Principle Dot plot are two dimensional graphs, showing a comarision of two sequences. The principle used to generate the dot plot is: The top X and the left y axes of a rectangular array are used to represent the two sequences to be compared. Calculation: Matrix • Columns = residues of sequence 1 • Rows = residues of sequence 2. A dot is plotted at every co-ordinate where there is similarity between the bases

10. Scoring Matrix Scoring system is a set of values for qualifying the set of one residue being substituted by another in an alignment . It is also known as substitution matrix. Scoring matrix of nucleotide is relatively simple. A positive value or a high score is given for a match & negative value or a low score is given for a mismatch. Scoring matrices for amino acids are more complicated because scoring has to reflect the physicochemical properties of amino acid residues.

11. Dynamic programming Method It was introduced by Richard Bellman in 1940. The word programming here denotes finding an acceptable plan of action not computer programming . It is useful in aligning nucleotides sequences of DNA and amino acid sequence of proteins coded by that DNA. Is solving complex problems by breaking them into a simpler sub problems. Problem can be divided into many smaller parts. Dynamic programming is a three step process that involves: 1) Initialization 2)Matrix Scoring (filling ) 3) Trace back and aligning

12. BLAST BLAST is stand for The Basic Local Alignment Search Tool is for comparing gene and protein sequences against others in public databases. BLAST is a set of sequence comparison algorithms used to search databases for optimal local alignments to a query . It breaks the query and databases sequences into fragments and seeks matches between them .

13. TYPES OF BLAST

14. References http://www.google.com / NCBI Handbook http://www.cs.mcgill.ca / https://www.slideshare.net/mobile/ammarkareem3/sequence-alignment-58496054 http://www.slideshare.net/mobile/zohaibkhan404/dynamic-programming-42984154