Clone-Array Pooled Shotgun Mapping and Sequencing: Design and Analysis of Experiments

Miklós Csürös[1] (csuros@iro.umontreal.ca)
Bingshan Li[2] (bli1@bcm.tmc.edu)
Aleksandar Milosavljevic[3] (amilosav@bcm.tmc.edu)

[1]Département d'informatique et de recherche opérationnelle, Université de Montréal, CP 6128 succ. Centre-Ville, Montréal, Québec H3C 3J7, Canada
[2] Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
[3] Bioinformatics Research Laboratory, Department of Molecular and Human Genetics, and Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine

Abstract

This paper studies sequencing and mapping methods that rely solely on pooling and shotgun sequencing of clones. First, we scrutinize and improve the recently proposed Clone-Array Pooled Shotgun Sequencing (CAPSS) method, which delivers a BAC-linked assembly of a whole genome sequence. Secondly, we introduce a novel physical mapping method, called Clone-Array Pooled Shotgun Mapping (CAPS-MAP), which computes the physical ordering of BACs in a random library. Both CAPSS and CAPS-MAP construct subclone libraries from pooled genomic BAC clones.

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