title: EULER-PCR: finishing experiments for repeat resolution.
abstract: Genomic sequencing typically generates a large collection of unordered contigs or scaffolds. Contig ordering (also known as gap closure) is a non-trivial algorithmic and experimental problem since even relatively simple-to-assemble bacterial genomes typically result in large set of contigs. Neighboring contigs maybe separated either by gaps in read coverage or by repeats. In the later case we say that the contigs are separated by pseudogaps, and we emphasize the important difference between gap closure and pseudogap closure. The existing gap closure approaches do not distinguish between gaps and pseudogaps and treat them in the same way. We describe a new fast strategy for closing pseudogaps (repeat resolution). Since in highly repetitive genomes, the number of pseudogaps may exceed the number of gaps by an order of magnitude, this approach provides a significant advantage over the existing gap closure methods.
authors.affiliation: Department of Computer Science and Engineering, University of California, San Diego, CA 92093, USA.
authors.forename: Zufar
authors.initials: Z
authors.lastname: Mulyukov
authors.forename: Pavel A
authors.initials: PA
authors.lastname: Pevzner
mesh_terms: D001483:Base Sequence; D004247:DNA / Q000737:chemistry / Q000235:genetics*; D017931:DNA Primers; D009345:Neisseria meningitidis / Q000235:genetics; D009690:Nucleic Acid Conformation; D016133:Polymerase Chain Reaction / Q000379:methods*; D012091:Repetitive Sequences, Nucleic Acid; D015203:Reproducibility of Results
chemical_list: D017931:DNA Primers; D004247:DNA