Algorithms for Combining Sequence Data with Optical Maps: Examples from P. falciparum and E. coli

Marco Antoniotti, Thomas S. Anantharaman, Chiung-Wen Chang, David C. Schwartz, Bud Mishra

Abstract

Current, genome wide shotgun sequence assembly methods have produced a very large amount of data that can eventually answer many important biological questions. Concurrently, our groups at NYU and University of Wisconsin have developed a Single Molecule approach to produce High-Resolution Ordered Restriction Maps (Optical Mapping) that can be integrated with the sequence data for the purposes described below:

1 - speed up the sequence assembly by providing an appropriate scaffolding and
2 - establish the correctness of a completed sequence assembly by aligning in silico restriction maps from sequences with the optical maps
3 - align, orient and phase sequence contigs and thus, facilitate the gap closing and finishing steps.

We ran our validation and alignment algorithms on the P. Falciparum and validated the assembly of chromosomes 2 and 3, while phasing the known contigs of other chromosomes.

We also ran our algorithms on the E. Coli K12 data and are able to suggest possible local improvements on the assembled sequence.