Efficient method for alignment of a polypeptide query against a collection of polypeptide subjects

摘要

The invention relates to a method that efficiently identifies segments of a collection of polypeptides which are similar to a query polypeptide. Candidate alignments of all or part of the query polypeptide with similar amino acid sequences from the collection of polypeptides are first identified using a scalable parallel processing filter algorithm. The candidate alignments are further examined to yield an ordered list of scored alignments. This method enables massive parallel processing with minimized logic requirements and maximized logic utilization to achieve a dramatic reduction in the time required to produce a high quality sequence alignment report with a fraction of the hardware resources required by current methods.