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Sequence Alignment

What is Sequence Alignment in Homology modelling?

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Sequence Alignment: This is the critical step in homology modeling. We have many methods for this. But we have to select a method based on our needs. We have considered some factors while choosing a method.

The factors are as bellow:

• Algorithm to be used
• Scoring matrices to be used
• Assignment of gap venalities

Homology modeling is based on dynamic programming algorithms. There are number of algorithms such as Needleman and Wunsch, Smith waterman and Blastp.The last one is different from others because it doesn’t allow any gaps. The scoring matrices of alignments are very typical matrices in which the identical amino acids are constructed in to a 20X20 matrix. We generally apply four types of general scorings to the alignments. They are:

• Identity
• Genetic code
• Chemical Similarity
• Observed Substitutions

Identity considers the residues that are identical. The genetic code considers changes in DNA and RNA which interconverts codons for the amino acids. Chemical similarity considers the physico-chemical properties with greater weight given to alignment of similar properties. The substitution frequencies observed in alignment of sequences are considered by observed substitutions. Substitution schemes are based on analysis of the frequency with which a given amino acid is observed to be replaced by another with which the sequence alignment is found, so these are considered to be the best methods of scoring alignments.

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