The problem of finding an optimal structural alignment for a pair of superimposed proteins is often amenable to the Smith-Waterman dynamic programming algorithm, which runs in time proportional to the product of the lengths of sequences being aligned. While the quadratic running time is acceptable for computing a single alignment of two, spatially “fixed”, structures, the time complexity become...

We consider the problem of similarity searches on protein databases based on both sequence and structure information simultaneously. Our program extracts feature vectors from both the sequence and structure components of the proteins. These feature vectors are then combined and indexed using a novel multi-dimensional index structure. For a given query, we employ this index structure to find can...

Deoxyribonucleic acid (DNA) is a molecule that encodes unique genetic instructions used in the development and functioning of all known living organisms and many viruses. This Genetic information is encoded as a sequence of nucleotides (adenine, cytosine, guanine, and thymine) recorded using the letters A, C, G, and T.DNA querying or alignment of these sequences required dynamic programming too...

In this paper we show how to significantly accelerate SmithWaterman protein sequence alignment algorithm using reprogrammable logic devices – FPGAs (Field Programmable Gate Array). Due to perfect sensitivity, the Smith-Waterman algorithm is important in a field of computational biology but computational complexity makes it impractical for large database searches when running on general purpose ...

We consider the problem of similarity searches on protein databases based on both sequence and structure information simultaneously. Our program extracts feature vectors from both the sequence and structure components of the proteins. These feature vectors are then combined and indexed using a novel multi-dimensional index structure. For a given query, we employ this index structure to find can...

Text-based search is widely used for biomedical data mining and knowledge discovery. Character errors in literatures affect the accuracy of data mining. Methods for solving this problem are being explored. This work tests the usefulness of the Smith-Waterman algorithm with affine gap penalty as a method for biomedical literature retrieval. Names of medicinal herbs collected from herbal medicine...