Algorithms of sequences alignment .......!

 Algorithms :- 

Alignment algorithms , both global and local , are fundamental similar and differ in the optimization strategy used in aligning similar residues .

There are two method :- 

1) Dot matrix method :-

- The most basic sequences alignment method is the dot matrix method .

- It is also known as the dot plot method .

- It is the graphical way of comparing two sequences in a two dimensional matrix.

- In dot matrix , two sequences to be compared are written in the horizontal and vertical axis of the matrix .

- The comparison is done by scanning each residue of one sequence for similarities with all residues in the other sequence.

- If residue match is found , a dot is placed within the graph .Otherwise the matrix position are left blank .

- When the two sequences have substantial region of similarity , many dots line up to form contiguous diagonal lines , which reveal the sequences alignment .

- If there are interruption in the middle of  a diagonal lines. they indicates insertions or deletions.

- Parallel diagonal lines within the matrix represent repetitive regions of the sequences .

Use of Dot matrix :- 

- The dot matrix method gives a direct visual statement of the relationship between two sequences and help easy identification of the region .

- The method thus has some application in genomics .

- It is useful in identification of chromosomal repeats and in comparing gene order conservation between two closely related genomes.

- It can be used in identification of nucleic acid secondary structure through detecting self complementarity of a sequences .

eg. of web servers for dot plots :- 

1) Dot matcher

2) Dot helix  

3) Matrix Plot.

2) Dynamic programming method :- 

Dynamic programming (DP) is a most fundamental programming technique in bioinformatics. Sequence comparison, gene recognition, RNA structure prediction and hundreds of other problems are solved by ever new variants of DP. Despite of all available experience, the development of the typical DP recurrences is nontrivial, and their implementation presents quite a few pitfalls. To quote a recent comment by an expert. 

- It is an exhaustive and quantitative method to find optimal alignments.

- It is a fundamentally similar to the dot matrix in that it also creates a two dimensional alignment grid.

- It find alignment in amore quantitative way by converting converting a dot matrix into a scoring matrix to account for matches and mismatches between sequences 

- Dynamic programing work by first constructing a two dimensional matrix whose axes are the two sequences to be compared .

Dynamic programing in sequences alignment there are three step in dynamic programming .

1) Initialization ;-

The first step in the global alignment dynamic programming approach is to create a matrix with M + 1 columns and N+1 rows where M and N correspond to size of the sequences to be aligned.

2) Matrix filling ( scoring ) :-

- Fill the matrix with highest possible score .

- To align with diagonal  ( align in next position )

-  Align in off diagonal requires insertion of cross ponding gap.

3) Trace back and aligning :-

- Move from last corner and follow arrow.