M Tech Dissertations
Permanent URI for this collectionhttp://drsr.daiict.ac.in/handle/123456789/3
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Item Open Access Exact algorithm for segment based sequence alignment(Dhirubhai Ambani Institute of Information and Communication Technology, 2015) Tailor, Divyesh; Divakaran, SrikrishnanIn bioinformatics, proteins, large biological molecules consisting long chain of amino acids, are described by a sequence of 20 amino acids. To analyze these protein sequences pairwise alignment is being used, which identify regions of similarity that may be a result of structural, functional and/or evolutionary relationship between them. Traditional pairwise alignment algorithms work on residue level; it does not account structural or functional information that protein carries. A new approach for protein sequence analysis is being proposed here, pairwise alignment of two protein sequences based on segments. Segments of the sequences can be formed on the basis of protein feature, i.e., functional sites or secondary structure of the protein. Each segment carries a type and weight for the alignment process. Algorithm should align two sequences such that segments with weight higher than threshold value must align with the similar type of segment and score for the alignment must be maximal for given scoring function. Here, we are proposing a generic framework to understand, explore and experiment proteins based on their features, i.e. structure, function, and evolution.Item Metadata only Heuristic approach for segment based pairwise sequence alignment in bioinformatics(Dhirubhai Ambani Institute of Information and Communication Technology, 2015) Desai, Jeet; Divakaran, Srikrishnan0Item Open Access Heuristics for pair-wise sequence alignment(Dhirubhai Ambani Institute of Information and Communication Technology, 2015) Patel, Dhara; Divakaran, SrikrishnanDevelop framework for pairwise alignment of given two sequences based on their feature. There may be situation in which sequences look different but share common structure, function or evolutionary related information. So, rather than forcing alignments to align residue-to-residue comparison, we align them based on segment-to-segment comparison where weight and type is given to each segment. Segments of protein sequence is given based on function, evolution or structure prediction tools. The proposed algorithm is work on proper alignment in higher weighted segments. The rest segments will align with faster existing algorithm so it makes execution faster. The common framework for all type of alignments with one algorithm is new idea. Benchmark Alignment dataBASE , BALIBASE[10] is used to compare result of proposed algorithm with available algorithms. The experiments shows that proposed method does not work for all test cases. But for dissimilar sequences, which looks different, for that proposed method gives good result in less amount of time compare to Needleman-Wunsch[18],Fasta[14] and Blast[24] algorithm.