Abstract: A method for assembling nucleic acid sequence fragments is disclosed. The fragments are assembled using information about their relative position inferred by comparison of the fragments against a known sequence of a related nucleic acid (FIG. 3). Additionally, the method localizes fragments to bacterial artificial chromosomes (FIG. 1) and determines relative position of bacterial artificial chromosomes using sequence comparison information (FIG. 6). The method utilizes the information about relative orientation, mutual distance, fragment localization to bacterial artificial chromosomes, and relative position of bacterial artificial chromosomes to constrain the assembly process (FIG. 5), thus resulting in a more accurate assembly requiring fewer sequencing reactions.

Abstract: Positional Hashing, a novel method for detecting similarities between texts such as DNA sequences, amino acid sequences, and texts in natural language is disclosed. The method is particularly well suited for large-scale comparisons such as that of mutual comparisons of millions of sequence fragments that result from mammalian-scale sequencing projects and for whole-genome comparisons of multiple mammalian genomes. Positional Hashing is carried out by breaking the sequence comparison problem along its natural structure, solving the subproblems independently, and then collating the solutions into an overall result. The decomposition of the problem into subproblems enables parallelization, whereby a large number of nodes in a computer cluster or a computer farm are concurrently employed on solving the problem without incurring the quadratic time performance penalty characteristic of prior art.