Swaati algorithm of alignment ppt

Comparative Study of Dynamic Comparative Study of Dynamic Programming Algorithm for Pairwise Programming Algorithm for Pairwise

Sequence AlignmentSequence Alignment

Submitted by:Swati KumariRoll no: 22M.Sc Bioinformatics2nd semesterSession: 2014-16

ContentsContents

Introduction Types of Alignment

Global Alignment Local Alignment Glocal Alignment

Comparitive Study of Pairwise Alignment

– Steps

• Initialization of matrix• Filling of matrix with maximum score• Trace back the residue for appropiate alignment

Time and Space Complexity Application

IntroductionIntroduction

Dynamic Algorithm -

“Sligthly different with Divide and Conqure” as it divide the set of problem into subset and the solution is commulative sum of solution.

The solution of first subset is the input of second subset overlapping solution.

It laso gives optimal solution.

Sequence Alignment -

Sequence alignment is the procedure of comparing two (pair‐wise alignment) or more multiple sequences (nucleotide and amino acid) by searching for a series of individual characters or patterns that are in the same order in the sequences.

Types of AlignmentTypes of Alignment

Global Alignment -

Also called Needleman-Wunsch Algorithm and NW Alignment.

Discovered by Needleman and Wunsch , 1981.

A global alignment contains all letters from both the query and target sequences. i..e., alignment of two sequence from head to tail which is roughly equal in length.

Local Alignment -

Also called Smith–Waterman algorithm and SW Alignment.

Discovered by Smith and Waterman algorithm , 1981.

A local alignment aligns a substring of the query sequence to a substring of the target sequence.

Use to detect the local region with high level of similarity of the two given sequences or dissimilar.

Glocal Alignment -

Also called Semi-global , Ends-free Alignment.

It is special case of Global Alignment i..e., Hybrid of Global and Local Alignment.

Attempt to find the best possible alignment that includes the start and end of one or the other sequence.

This can be especially useful when the downstream part of one sequence overlaps with the upstream part of the other sequence.


Initilization of Matrix :-

(m*n)+1 (m*n)+1 (m*n)

Base Condition :-

V(i,o) = Σ = σ ( Sk,_ )

V(j,so) = Σ = σ ( _,Tk )

∀i, j. V (i, 0) = 0 ,

V (0, j) = 0 Same as Local

Comparitive Study of Pairwise AlignmentComparitive Study of Pairwise Alignment

i

i

k=0

k=0


Filling of Matrix with Maximum score :-Recurrence relation : -

V( i,j ) = max V ( i-1,j-1 ) + σ ( Si,Tj ) V ( i-1,j ) + σ ( Si,_j ) V ( i,j-1 ) + σ ( _,Tj )

V( i,j ) = max 0 V ( i-1,j-1 ) + σ ( Si,Tj ) V ( i-1,j ) + σ ( Si,_j ) V ( i,j-1 ) + σ ( _,Tj )

Same as Global Alignment

Global Alignment Local Alignment Local Alignment

Trace Back the Residue for appropiate alignment :-

Rule for Trace Back :-

Start with last row and last column of the matrix

Start with those indices which have max matrix Same as Local

AlignmentPlace the back pointer to cell from where the max score is obtain

Place the back pointer to cell from where the max score is obtain

Go to the first column and first row by doing same

Go to the indices having minimum score

Global Alignment Local Alignment Local Alignment

Optimal Alignment :-

S = d b c d aT = b b _ d a

S = a t g c a t tT = _ t a c _ t t

S = _t g c t t g T = t t g a t _ _

Time and Space Complexity :-

O (n*m) Time = O(n*m)Space = O(n+m)

Same as Local alignmet

Application : -

To find homology between two sequence i..., full length sequence.

To find domain and motive i..e local region in seuqence .

To find the Shotgun sequence.

ReferencesReferences

http://en.wikipedia.org/wiki/Sequence_alignment

http://www.srmuniv.ac.in/sites/default/files/files/5%286%29.pdf


ReferencesReferences


http://www.srmuniv.ac.in/sites/default/files/files/5%286%29.pdf


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Swaati algorithm of alignment ppt