sequence alignment author:- aya osama supervision:- dr.noha khalifa

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Sequence Alignment

Author:- Aya Osama Supervision:- Dr.Noha khalifa

Sequence Alignment Variants

variants of sequence alignment: Global alignment (The Needelman-

Wunsch Algorithm)

Local alignment (The Smith-Waterman Algorithm)

Blast Alignment(basic local alignment tool)

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Global Sequence Alignment It is an example of dynamic programming, and was

the first application of dynamic programming to biological sequence comparison

Suitable when the two sequences are of similar length, with a significant degree of similarity throughout

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Local Sequence Alignment Useful for dissimilar sequences that are suspected

to contain regions of similarity or similar sequence motifs within their larger sequence context

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Sequence ComparisonMuch of bioinformatics involves sequences DNA sequences RNA sequences Protein sequences

We can think of these sequences as strings of letters DNA & RNA: |alphabet|=4 Protein: |alphabet|=20

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Global AlignmentInput: two sequences over the same alphabetOutput: an alignment of the two sequences

Example: GCGCATGGATTGAGCGA and TGCGCCATTGATGACCA A possible alignment:

-GCGC-ATGGATTGAGCGATGCGCCATTGAT-GACC-A

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-GCGC-ATGGATTGAGCGATGCGCCATTGAT-GACC-A

Three elements: Perfect matches Mismatches Insertions & deletions (indel)

Global Alignment

Example (cont):

Symmetric view of evolution

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Score each position independently: Match: +1 Mismatch: -1 Indel: -2Score of an alignment is sum of position scores

Global Alignmentscoring scheme

Example: -GCGC-ATGGATTGAGCGATGCGCCATTGAT-GACC-A

Score: (+1x13) + (-1x2) + (-2x4) = 3

------GCGCATGGATTGAGCGATGCGCC----ATTGATGACCA--Score: (+1x5) + (-1x6) + (-2x11) = -23

How to make alignment between two sequences?

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How to make alignment between two sequences?(cont’d)

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How to make alignment between two sequences?(cont’d)

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How to make alignment between two sequences?(cont’d)

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How to make alignment between two sequences?(cont’d)

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How to make alignment between two sequences?(cont’d)

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How to make alignment between two sequences?(cont’d)

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Refrences

www.wikipedia.comhttp://seqtool.sdsc.edu/CGI/BW.cgi#!

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Thanks Any Questions??

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