MOTIVATION: A considerable amount of human intervention is currently required to produce high-quality fingerprint-based physical maps for genomic studies. RESULTS: An algorithm has been developed and implemented to automatically order fingerprinted clones within contigs. The resulting software, named CORAL (Clone ORdering ALgorithm), has been tested on maps that have previously been manually edited and on maps derived from in silico simulations. The fingerprint map and DNA sequence of the human genome has provided an additional test to CORAL. Measurements suggest that CORAL performs significantly better than the software currently used by most laboratories to order fingerprinted clones at throughputs far exceeding those that can be achieved manually.
MOTIVATION: A considerable amount of human intervention is currently required to produce high-quality fingerprint-based physical maps for genomic studies. RESULTS: An algorithm has been developed and implemented to automatically order fingerprinted clones within contigs. The resulting software, named CORAL (Clone ORdering ALgorithm), has been tested on maps that have previously been manually edited and on maps derived from in silico simulations. The fingerprint map and DNA sequence of the human genome has provided an additional test to CORAL. Measurements suggest that CORAL performs significantly better than the software currently used by most laboratories to order fingerprinted clones at throughputs far exceeding those that can be achieved manually.
Authors: Warren M Snelling; Readman Chiu; Jacqueline E Schein; Matthew Hobbs; Colette A Abbey; David L Adelson; Jan Aerts; Gary L Bennett; Ian E Bosdet; Mekki Boussaha; Rudiger Brauning; Alexandre R Caetano; Marcos M Costa; Allan M Crawford; Brian P Dalrymple; André Eggen; Annelie Everts-van der Wind; Sandrine Floriot; Mathieu Gautier; Clare A Gill; Ronnie D Green; Robert Holt; Oliver Jann; Steven Jm Jones; Steven M Kappes; John W Keele; Pieter J de Jong; Denis M Larkin; Harris A Lewin; John C McEwan; Stephanie McKay; Marco A Marra; Carrie A Mathewson; Lakshmi K Matukumalli; Stephen S Moore; Brenda Murdoch; Frank W Nicholas; Kazutoyo Osoegawa; Alice Roy; Hanni Salih; Laurent Schibler; Robert D Schnabel; Licia Silveri; Loren C Skow; Timothy Pl Smith; Tad S Sonstegard; Jeremy F Taylor; Ross Tellam; Curtis P Van Tassell; John L Williams; James E Womack; Natasja H Wye; George Yang; Shaying Zhao Journal: Genome Biol Date: 2007 Impact factor: 13.583
Authors: Benjamin J Raphael; Stanislav Volik; Peng Yu; Chunxiao Wu; Guiqing Huang; Elena V Linardopoulou; Barbara J Trask; Frederic Waldman; Joseph Costello; Kenneth J Pienta; Gordon B Mills; Krystyna Bajsarowicz; Yasuko Kobayashi; Shivaranjani Sridharan; Pamela L Paris; Quanzhou Tao; Sarah J Aerni; Raymond P Brown; Ali Bashir; Joe W Gray; Jan-Fang Cheng; Pieter de Jong; Mikhail Nefedov; Thomas Ried; Hesed M Padilla-Nash; Colin C Collins Journal: Genome Biol Date: 2008-03-25 Impact factor: 13.583