Functional proteomics with biolinguistic methods

In this article, new algorithms for comparative proteomics using extensions of n-gram analysis are described. Results demonstrate that these algorithms are more sensitive than those currently available for both genomics and proteomics analysis, enabling a more accurate portrayal of similarity of gene function. The algorithms allow the comparison of protein sequences using biochemical properties that enable the protein molecules to fold and perform the necessary functions. The algorithms described are amenable to parallelization with effective domain database partitioning. This makes them an attractive alternative for searching protein databases by developing high-speed, functionally partitioned searches.