Using LTC Software for Physical Mapping and Assisting in Sequence Assembly

To facilitate pseudomolecule sequence assembly based on sequencing of BAC-clones from minimal tilling paths (MTPs), physical contigs should be ordered (and oriented) along the chromosome. Previously we presented an analytical system LTC enabling construction of long reliable physical contigs and MTP selection/curing avoiding putatively chimerical clones. We extended LTC by tools for in silico fingerprinting of individually sequences clones or pools of several overlapping clones. Comparison of these in silico fingerprints with in vitro fingerprints same clones and their neighbors in the contig can be used for testing the quality of clone sequencing and for ordering of long sequence contigs (>10 kb) within the clone(s). In addition, we demonstrate the advantages of using topology of the network structure analysis developed in LTC for identification of pseudo-linkage in construction of genetic maps as well as for building of radiation hybrid maps. These results can assist in anchoring of physical contigs to integral map of the chromosome.