PABS: An online platform to assist BAC-by-BAC sequencing projects. (January 2008)

• Record Type: Journal Article
• Authors: Todesco, Sara; Campagna, Davide; Levorin, Fabrizio; D'Angelo, Michela; Schiavon, Riccardo; Valle, Giorgio; Vezzi, Alessandro
• Is Part Of: Biotechniques. Volume 44:Number 1(2008)
• Page Start: 60
• Page End: 64
• Publication Date: 2008-01
• Subjects: Biology, Experimental -- Periodicals; Molecular biology -- Periodicals; Medical technology -- Periodicals; Biology, Experimental; Medical technology; Molecular biology; Clinical Laboratory Techniques -- Periodicals; Research -- Periodicals; Medical Laboratory Science -- Periodicals; Periodicals; Electronic journals; 570
• DOI: 10.2144/000112686
• Languages: English
• ISSNs: 0736-6205

Abstract

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.