SequencePad™ offers a sophisticated user interface for building and editing multiple sequence alignments through an interactive phylogenetic tree. It automatically applies BLAST to retrieve known sequences for the protein, and ClustalW to align the entire set. Evolutionary conservation values are then calculated for each amino acid using the PET91 scoring table. Functional sites on proteins are well known to vary less than other sites, as illustrated below by the CheA-CheY complex. The two proteins are shown in tube and surface renderings, respectively. Blue amino acids have lower smoothed conservation values than white ones. Red amino acids are <10% exposed to solvent and are ignored in this calculation.
SequencePad's features list includes annotation profiling, an interactive phylogenetic tree for selection, and visualization in the SPADE Molecular Viewer. SequencePad provides profile generating equipment based on key words from sequence headers. This allows inclusion by e.g. function annotations, and exclusion by terms that indicate e.g. deliberate mutation. After calculating conservation, SPADE's automated color-by-value menu functions are taken advantage of to provide several options for coloring the atoms, tubes, and surfaces of visualized protein structures. SequencePad was created by Russ Block and Deacon Sweeney, with the Bioinformatics Research Group at Wright State University.