# Sequence Analysis

These heuristic approaches apply word matching and hash tables in their implementation unlike dynamic programming that are rigorous mathematical approaches. Computational biology attempts to compare nucleotide or protein sequence to analyze either their difference or similarities at the level of bases or amino acids. This information is gathered with the objective of inferring structural, functional and evolutionary relationship among the sequences being analyzed (Baxevanis and Oullette, 2001). Sequence alignment enables one to map residues (nucleotides or amino acids) of two or more sequences. There are two methods of sequence alignment, pairwise alignment and multiple alignments.

Whereas pairwise alignments involve two sequences, multiple alignments involve more than two sequences. In sequence alignment, various alignments are made to cater for the differences between any two or more sequences being aligned. Residues which are aligned but not identical may represent substitution in the evolution path. In other cases regions of the sequences where they aligned with other sequences in the alignment but they have no common residues may represent insertion I the evolution process. Sequence alignments will represent regions that are highly identical (highly conserved) than other alignment regions.

These areas are suggestive of residues which may play crucial role to the structural and functional integrity of the expressed gene product either an RNA or protein. Materials and Methods Dynamic Programming Provided with two sequences AGQDEASY and AGCDEESW, an identity relation was used to construct a comparison matrix (1 if i=j, 0 otherwise). The dynamic programming method proceeded through three stages. Firstly, the two sequences were placed on two axes of a grid and the matrix filled to indicate the relationship between each residue in sequence 1 with all residues in sequence 2. Then, the comparison matrix is converted in to the ‘maximum match matrix’, which indicates the highest scoring path starting from a given residue.

Here we start from the bottom right hand corner of the comparison matrix; the score in a particular grid point is added to the highest scoring box in the following row and column. Once this has been done, the highest scoring path can be extracted from the matrix, defining the alignment. Comparison Matrix A G Q D E A S Y A G C D E E S W Maximum match matrix A G Q D E A S Y A G C D E E S W Sequence and structure analysis Pairwise alignment of the provided two protein sequences was implemented using Blastp algorithm available at the NCBI websites (Altschul et al. , 1997).

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