Homologous proteins are often compared by pairwise sequence alignment, and structure superposition if the atomic coordinates available. Unification of data is an important task in structural biology. Here, we present Sequence Similarity 3D (SS3D) method integrating information. SS3D a distance substitution matrix-based for straightforward visualization regions similarity difference between homo...

Sequence comparison, a vital research tool in computational biology, is based on a simple O(n2) algorithm that easily maps to a linear array of processors. This paper reviews and compares high-performance sequence analysis on general-purpose supercomputers and single-purpose reconfigurable, and programmable co-processors. The difficulty of comparing hardware from published performance figures i...

MOTIVATION This paper presents LASSAP, a new software package for sequence comparison. LASSAP is a programmable, high-performance system designed to raise current limitations of sequence comparison programs in order to fit the needs of large-scale analysis. LASSAP provides an API (Application Programming Interface) allowing the integration of any generic pairwise-based algorithm. RESULTS What...