%0 Journal Article %J Nature %D 2004 %T A physical map of the chicken genome. %A Wallis, John W %A Aerts, Jan %A Groenen, Martien A M %A Crooijmans, Richard P M A %A Layman, Dan %A Graves, Tina A %A Scheer, Debra E %A Kremitzki, Colin %A Fedele, Mary J %A Mudd, Nancy K %A Cardenas, Marco %A Higginbotham, Jamey %A Carter, Jason %A McGrane, Rebecca %A Gaige, Tony %A Mead, Kelly %A Walker, Jason %A Albracht, Derek %A Davito, Jonathan %A Yang, Shiaw-Pyng %A Leong, Shin %A Chinwalla, Asif %A Sekhon, Mandeep %A Wylie, Kristine %A Dodgson, Jerry %A Romanov, Michael N %A Cheng, Hans %A De Jong, Pieter J %A Osoegawa, Kazutoyo %A Nefedov, Mikhail %A Zhang, Hongbin %A McPherson, John D %A Krzywinski, Martin %A Schein, Jacquie %A Hillier, LaDeana %A Mardis, Elaine R %A Wilson, Richard K %A Warren, Wesley C %K Animals %K Chickens %K Chromosomes, Artificial, Bacterial %K Cloning, Molecular %K Contig Mapping %K DNA Fingerprinting %K Genetic Linkage %K Genome %K Genomics %K Physical Chromosome Mapping %K Sequence Tagged Sites %X

Strategies for assembling large, complex genomes have evolved to include a combination of whole-genome shotgun sequencing and hierarchal map-assisted sequencing. Whole-genome maps of all types can aid genome assemblies, generally starting with low-resolution cytogenetic maps and ending with the highest resolution of sequence. Fingerprint clone maps are based upon complete restriction enzyme digests of clones representative of the target genome, and ultimately comprise a near-contiguous path of clones across the genome. Such clone-based maps are used to validate sequence assembly order, supply long-range linking information for assembled sequences, anchor sequences to the genetic map and provide templates for closing gaps. Fingerprint maps are also a critical resource for subsequent functional genomic studies, because they provide a redundant and ordered sampling of the genome with clones. In an accompanying paper we describe the draft genome sequence of the chicken, Gallus gallus, the first species sequenced that is both a model organism and a global food source. Here we present a clone-based physical map of the chicken genome at 20-fold coverage, containing 260 contigs of overlapping clones. This map represents approximately 91% of the chicken genome and enables identification of chicken clones aligned to positions in other sequenced genomes.

%B Nature %V 432 %P 761-4 %8 2004 Dec 09 %G eng %N 7018 %1 https://www.ncbi.nlm.nih.gov/pubmed/15592415?dopt=Abstract %R 10.1038/nature03030 %0 Journal Article %J Genome Res %D 2003 %T Software for automated analysis of DNA fingerprinting gels. %A Fuhrmann, Daniel R %A Krzywinski, Martin I %A Chiu, Readman %A Saeedi, Parvaneh %A Schein, Jacqueline E %A Bosdet, Ian E %A Chinwalla, Asif %A Hillier, LaDeana W %A Waterston, Robert H %A McPherson, John D %A Jones, Steven J M %A Marra, Marco A %K Animals %K Cattle %K Chromosomes, Artificial, Bacterial %K DNA %K DNA Fingerprinting %K Gels %K Mice %K Models, Chemical %K Rats %K Sepharose %K Software %X

Here we describe software tools for the automated detection of DNA restriction fragments resolved on agarose fingerprinting gels. We present a mathematical model for the location and shape of the restriction fragments as a function of fragment size, with model parameters determined empirically from "marker" lanes containing molecular size standards. Automated identification of restriction fragments involves several steps, including: image preprocessing, to put the data in a form consistent with a linear model; marker lane analysis, for determination of the model parameters; and data lane analysis, a procedure for detecting restriction fragment multiplets while simultaneously determining the amplitude curve that describes restriction fragment amplitude as a function of mobility. In validation experiments conducted on fingerprinted and sequenced Bacterial Artificial Chromosome (BAC) clones, sensitivity and specificity of restriction fragment identification exceeded 96% on restriction fragments ranging in size from 600 base pairs (bp) to 30,000 bp. The integrated suite of software tools, written in MATLAB and collectively called BandLeader, is in use at the BC Cancer Agency Genome Sciences Centre (GSC) and the Washington University Genome Sequencing Center, and has been provided to the Wellcome Trust Sanger Institute and the Whitehead Institute. Employed in a production mode at the GSC, BandLeader has been used to perform automated restriction fragment identification for more than 850,000 BAC clones for mouse, rat, bovine, and poplar fingerprint mapping projects.

%B Genome Res %V 13 %P 940-53 %8 2003 May %G eng %N 5 %1 https://www.ncbi.nlm.nih.gov/pubmed/12727910?dopt=Abstract %R 10.1101/gr.904303