This document discusses global and local sequence alignment. It introduces sequence alignment and its uses in identifying similarities between sequences that could indicate functional or evolutionary relationships. It describes the principles of alignment and the different types of alignment, including global alignment, which aligns entire sequences, and local alignment, which matches regions of similarity. Methods for alignment include dot plots, scoring matrices, and dynamic programming. BLAST is introduced as a tool for comparing sequences against databases using local alignment algorithms.

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

2. Outline
• 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. Principle
• 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

16. 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