%0 Journal Article
%T A compartmentalized approach to the assembly of physical maps
%A Serdar Bozdag
%A Timothy J Close
%A Stefano Lonardi
%J BMC Bioinformatics
%D 2009
%I BioMed Central
%R 10.1186/1471-2105-10-217
%X We propose a novel compartmentalized method for the assembly of high quality physical maps from fingerprinted clones. The knowledge of genetic markers enables us to group clones into clusters so that clones in the same cluster are more likely to overlap. For each cluster of clones, a local physical map is first constructed using FingerPrinted Contigs (FPC). Then, all the individual maps are carefully merged into the final physical map. Experimental results on the genomes of rice and barley demonstrate that the compartmentalized assembly produces significantly more accurate maps, and that it can detect and isolate clones that would induce "chimeric" contigs if used in the final assembly.The software is available for download at http://www.cs.ucr.edu/~sbozdag/assembler/ webciteA physical map is a linear ordering of a set of overlapping clones in a genomic library. Physical maps are obtained from processing the signatures or fingerprints of all the clones in a library. Fingerprints can be generated by digesting clones with one or more restriction enzymes, or by hybridizing them to a carefully designed set of DNA probes. The computational problem is to build an overlap map of the clones that is consisted with the fingerprint data [1].Physical maps have been historically one of the cornerstones of genome sequencing projects. For instance, in clone-by-clone sequencing, first a physical map is constructed; then, a minimum-cardinality set of overlapping clones that spans the genomic region represented by the physical map, called minimal tiling path (MTP), is selected. Finally, the clones in the MTP are sequenced one by one [2]. The clone-by-clone sequencing method has been used to sequence several genomes including C. elegans [3], A. thaliana [4], H. sapiens [5], and O. sativa [6]. In several recent whole-genome shotgun sequencing projects, physical maps have also been employed to validate and improve the quality of sequence assembly [7]. This validation step has been used,
%U http://www.biomedcentral.com/1471-2105/10/217