Dynamic building of a BAC clone tiling path for the Rat Genome Sequencing Project.

TitleDynamic building of a BAC clone tiling path for the Rat Genome Sequencing Project.
Publication TypeJournal Article
Year of Publication2004
AuthorsChen, R, Sodergren, E, Weinstock, GM, Gibbs, RA
JournalGenome Res
Date Published2004 Apr
KeywordsAnimals, Chromosomes, Artificial, Bacterial, Computational Biology, Contig Mapping, DNA Fingerprinting, Genome, Rats, Sequence Analysis, DNA, Software

CLONEPICKER is a software pipeline that integrates sequence data with BAC clone fingerprints to dynamically select a minimal overlapping clone set covering the whole genome. In the Rat Genome Sequencing Project (RGSP), a hybrid strategy of "clone by clone" and "whole genome shotgun" approaches was used to maximize the merits of both approaches. Like the "clone by clone" method, one key challenge for this strategy was to select a low-redundancy clone set that covered the whole genome while the sequencing is in progress. The CLONEPICKER pipeline met this challenge using restriction enzyme fingerprint data, BAC end sequence data, and sequences generated from individual BAC clones as well as WGS reads. In the RGSP, an average of 7.5 clones was identified from each side of a seed clone, and the minimal overlapping clones were reliably selected. Combined with the assembled BAC fingerprint map, a set of BAC clones that covered >97% of the genome was identified and used in the RGSP.

Alternate JournalGenome Res.
PubMed ID15060010
PubMed Central IDPMC383313
Grant ListHG02395 / HG / NHGRI NIH HHS / United States