PABS: an online platform to assist BAC-by-BAC sequencing projects.
Genome sequencing projects are either based on whole genome shotgun (WGS) or on a BAC-by-BAC strategy. Although WGS is in most cases the preferred choice, sometimes the BAC-by-BAC approach may be better because it requires a much simpler assembly process. Furthermore, when the study is limited to specific regions of the genome, the WGS would require an unjustified effort, making the BAC-by-BAC the only feasible strategy. In this paper we describe an informatics pipeline called PABS (Platform Assisted BAC-by-BAC Sequencing) that we developed to provide a tool to optimize the BAC-by-BAC sequencing strategy. PABS has two main functions: (i) PABS-Select, to choose suitable overlapping clones; and (ii) PABS-Validate, to verify whether a BAC under analysis is actually overlapping the neighboring BAC.
Todesco
Sara
S
Department of Biology, University of Padova, Italy.
Campagna
Davide
D
Levorin
Fabrizio
F
D'Angelo
Michela
M
Schiavon
Riccardo
R
Valle
Giorgio
G
Vezzi
Alessandro
A
D001483:Base Sequence; D022202:Chromosomes, Artificial, Bacterial / Q000235:genetics*; D019295:Computational Biology / Q000379:methods*; D018745:Genome, Plant; D020407:Internet; D018551:Solanum lycopersicum / Q000235:genetics; D008969:Molecular Sequence Data; D017422:Sequence Analysis, DNA / Q000379:methods*