RIAZ Tariq

CMDWave: Conserved motifs detection using wavelets

Published date : 08 Jul 2005

CMDWave (Conserved Motif Detection using WAVElets) is a web server that predicts conserved motifs in protein sequences. A set of query protein sequences are first aligned using ClustalW to obtain equal sized sequences. CMDWave then converts the sequences into a numerical representation using electron-ion interaction potential (EIIP). This is followed by a wavelet decomposition and reconstruction. A new similarity metric along with thresholding is then used to identify conserved motifs across all the query sequences. Users need not specify the number of motifs to be identified.

type
Journal Paper
journal
In Silico Biology. 2005;5(4):415-8
Impact Factor
NIL

A tabu search algorithm for post processing multiple sequence alignment

Published date : 01 Jan 2004

Tabu search is a meta-heuristic approach that is proven to be useful in solving combinatorial optimization problems. We implement the adaptive memory features of tabu search to refine a multiple sequence alignment. Adaptive memory helps the search process to avoid local optima and explores the solution space economically and effectively without getting trapped into cycles. The algorithm is further enhanced by introducing extended tabu search features such as intensification and diversification.

type
Journal Paper
journal
Journal of Bioinformatics and Computational Biology, 2004
Impact Factor
NIL