Biomedical subjects

Tariq Riaz

Publications and source records attributed to Tariq Riaz.

3 recordsLinked to original sources

PubMed2005

WebAllergen: a web server for predicting allergenic proteins.

UNLABELLED: WebAllergen is a web server that predicts the potential allergenicity of proteins. The query protein will be compared against a set of prebuilt allergenic motifs that have been obtained from 664 known allergen proteins. The query will also be compared with known allergens that do not have detectable allergenic motifs. Moreover, users are allowed to upload their own allergens as alternative training sequences on which a new set of allergenic motifs will be built. The query sequences can also be compared with these motifs. AVAILABILITY: http://weballergen.bii.a-star.edu.sg/

Algorithms↗

PubMed2005

A tabu search algorithm for post-processing multiple sequence alignment.

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. The neighborhoods of a solution are generated stochastically and a consistency-based objective function is employed to measure its quality. The algorithm is tested with the datasets from BAliBASE benchmarking database. We have observed through experiments that tabu search is able to improve the quality of multiple alignments generated by other software such as ClustalW and T-Coffee. The source code of our algorithm is available at http://www.bii.a-star.edu.sg/~tariq/tabu/.

Algorithms↗

PubMed2005

CMDWave: conserved motifs detection using wavelets.

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. For larger groups of sequences, results can be emailed to the users.

Amino Acid Motifs↗