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Topic: Whole genome shotgun

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	Shotgun Cloning \| World of Microbiology and Immunology
		Shotgun sequencing was initially used to sequence small genomes such as that of the cauliflower mosaic virus (CMV), which is 8kb long.
		For example, a part of the fly genome was sequenced by the one-by-one approach and the whole genome shotgun method.
		The whole genome shotgun method generated the sequence much more quickly, but the one-by-one approach is probably more accurate because the genes were studied in more detail.
	www.bookrags.com /research/shotgun-cloning-wmi (462 words)

	Shotgun Sequencing (Site not responding. Last check: 2007-08-17)
		The shotgun part comes from the way the clone is prepared for sequencing: it is randomly sheared into small pieces (usually about 1 kb) and subcloned into a "universal" cloning vector.
		Genomic DNA is sheared or restricted to yield random fragments of the required size.
		The main limitation in this whole genome shotgun approach are the generation of fully representative small insert libraries and the computing power needed to generate the fully contiguous sequence from tens to hundreds of thousands of individual sequence reads.
	nema.cap.ed.ac.uk /teaching/genomics/Genomics3.html (726 words)

	Genome Biology \| Full text \| Finishing a whole-genome shotgun: Release 3 of the Drosophila melanogastereuchromatic ...
		The improvements made to the genomic sequence in Release 3 had a large impact on the annotation of transposable elements [9] because of the substantial corrections made in the assembly of repeated sequences.
		Because the non-repetitive regions of the genome were generally of good quality in Release 2, most of the improvements to the annotation of these regions resulted from the increased amounts of EST and cDNA data [7].
		Shotgun libraries of PCR products were constructed as the other libraries but without the size-selection step and with an increase in the shearing pressure from 10 to 20 psi and increase in time from 2 to 5 min.
	genomebiology.com /2002/3/12/research/0079 (9227 words)

	Shotgun sequencing Summary
		Shotgun sequencing is a method used in genetics for sequencing long DNA strands.
		Assembly of complex genomes is additionally aggravated by the great abundance of repetitive sequence, meaning similar short reads could come from completely different parts of the sequence.
		Proponents of this approach argue that it is possible to sequence the whole genome at once using large arrays of sequencers, which makes the whole process much more efficient than more traditional approaches.
	www.bookrags.com /Shotgun_sequencing (1086 words)

	Genome Biology \| Full text \| Heterochromatic sequences in a Drosophila whole-genome shotgun assembly
		Heterochromatin is concentrated in megabase-sized tracts in the centric and subtelomeric regions of the chromosomes.
		For example, a hallmark of heterochromatin is a high density of transposable elements, and the density of these elements in the genomic sequence increases continuously toward the centric ends of the euchromatic portions of the chromosome arms [12,31,32].
		The scaffold lies approximately 100 kb proximal to the end of the Release 3 euchromatic sequence of 2L [47] as determined by genomic Southern blots using single-copy probes derived from the ends of the scaffold and the Release 3 2L sequence [61].
	genomebiology.com /2002/3/12/research/0085 (7700 words)

	[No title]
		The whole genome shotgun method is a strategy that skips the laborious and time-consuming mapping process of the hierarchical shotgun approach by reassembling random fragments taken from the genome as a whole using computer algorithms (Figure 3.).
		In the hierarchical shotgun approach, the entire genome is shredded into large fragments of several hundred thousands bases, and these large fragments are then positioned on the genome chromosomes by looking for distinctive marker sequences, whose locations have already been pinpointed (mapping process).
		The strategy (the whole genome shotgun strategy) involves the use of a modular sequencing system from sample preparation to assembly of sequencing data(16) (Figure 4.).
	www.takeda-foundation.jp /en/award/takeda/2001/fact/02_4.html (825 words)

	JGI Genome Portal Help: What is a Scaffold?
		A scaffold is a portion of the genome sequence reconstructed from end-sequenced whole-genome shotgun clones.
		The goal of whole-genome shotgun assembly is to represent each genomic sequence in one scaffold; however, this is not always possible.
		For example, in polymorphic genomes, regions with a high density of allelic differences between haplotypes may be split into separate sets of scaffolds, each representing one allele.
	genome.jgi-psf.org /help/scaffolds.html (285 words)

	Genome Mapping Abstracts 1999
		Whole genome maps enable the size of the genome to be accurately determined, an important prelude to any sequencing endeavor.
		Most importantly, whole genome maps from genomic DNA provide an in situ picture of the architecture of the entire genome, revealing the number of chromosomes, existence of extrachromosomal elements etc. Populations can be potentially be characterized by comparing maps from different strains.
		Given the success we enjoyed in the restriction mapping of whole microbial genomes, and the proven reliability of the contig assembly algorithms developed for these efforts, we decided to construct a reference restriction map of the entire human genome.
	genome.gsc.riken.go.jp /hgmis/publicat/99santa/55.html (467 words)

	SEQUENCING THE GENOME (Site not responding. Last check: 2007-08-17)
		The other technique, known as whole genome shotgun sequencing, brings speed into the picture, enabling researchers to do the job in months to a year.
		Multiple copies of the genome are randomly shredded into pieces that are 2,000 base pairs (bp) long by squeezing the DNA through a pressurized syringe.
		The whole collection of BACs containing the entire human genome is called a BAC library, because each BAC is like a book in a library that can be accessed and copied.
	www.genomenewsnetwork.org /articles/06_00/sequence_primer.shtml (813 words)

	Plasmodium falciparum Genome Project
		To maximise the benefits to the scientific community of Plasmodium genome sequencing, the Pathogen Sequencing Unit is committed to the curation of Plasmodium spp.
		To facilitate comparative genomic analyses and to circumvent possible artefacts resulting from the study of laboratory cultured strains we have extended our analyses to a clinical isolate obtained from a female patient at St Georges Hospital London.
		Initial publication analysing the whole genome shotgun sequence for polymorphisms is planned.
	www.sanger.ac.uk /Projects/P_falciparum (715 words)

	Highlights: Bioscience: The Whole Fly
		Venter hoped to demonstrate that a technique called whole-genome shotgun sequencing, previously successful with microbes, could work for the much larger and more complex genomes of higher organisms—an essential step in his plan to apply the technique to the human genome.
		melanogaster’s genome, with 120 million bases, is intermediate in size between microbes and humans—and when finished, the accuracy of the whole-genome shotgun sequence could be checked against the existing data, including 28 million bases of finished sequence and completed physical maps.
		Whole-genome shotgun sequencing involves determining the sequence of millions of small cloned pieces of DNA that represent all of an organism’s genome in multiple overlapping stretches.
	www.lbl.gov /Science-Articles/Research-Review/Highlights/2000/stories/bioscience/wholefly2.html (941 words)

	The Human Genome Project (Site not responding. Last check: 2007-08-17)
		The Human Genome Project was launched in 1990 with the goal of sequencing the entire human genome - all 3 billion nucleotide pairs - by 2005 at an estimated cost of $3 billion.
		And critics of the whole-genome shotgun sequencing strategy argue that there may well be over 100,000 gaps, which will have to be filled in by the more methodical approaches being used in the other laboratories.
		Still, the tangible benefits of genomic research - from predicting risk for hereditary diseases to developing new drugs designed for an individual's genetic makeup - are still years away.
	library.thinkquest.org /C006188/research/genome.htm (543 words)

	Ask A Scientist - Shotgun cloning method
		The whole-genome shotgun sequencing method has been made feasible by recent advances in sequencing technology and in computational methods designed to assemble contiguous stretches of DNA from a large pool of overlapping shorter fragments.
		Recent release of the completed Drosophila genome sequence and an announcement on April 6, 2000, of the completion of the human genome sequence for one person by Celera are clear demonstrations of the feasibility of such approach.
		The shotgun approach uses random cloning of relatively small pieces of genomic DNA and subsequent sequencing of many clones to provide 10- to 12-fold coverage of the whole genome length.
	www.hhmi.org /cgi-bin/askascientist/highlight.pl?kw=&file=answers/genetics/ans_021.html (797 words)

	Whole Genome Sequence Validation – Accelerate Sequence Finishing
		In fact, entire regions of a genome could be excluded from the "finished" sequence because of budget limitations and lack of physical maps.
		At the end of the shotgun process, the investigator is left with a collection of sequence contigs.
		The addition of a whole genome physical map provides a scaffold for orienting these contigs.
	www.opgen.com /applications_sequence.aspx (453 words)

	Sequencing Medicago truncatula at the University of Oklahoma
		A pilot project to test the feasibility of a Whole Genome Shotgun sequencing project in collaboration with Rick Dixon, Greg May, Lloyd Sumner and Bob Gonzales at the Noble Foundation, Ardmore, Oklahoma began in the Spring of 2001.
		The initial goal of the Medicago truncatula genome project is to generate approximately 1-fold whole genome shotgun sequence data from a double-stranded pUC-based genomic library and obtain target shotgun clones for additional primer walking-based sequencing after analysis vs the ~100,000 Medicago truncatula ESTs and the genome of Arabidopsis thaliana.
		Our whole genome shotgun approach is allowing us to obtain the sequence of the Medicago truncatula chloroplast genome, since the total genomic DNA preparation not only contains the nuclear genome, but also a significant level of the chloroplast genome.
	www.genome.ou.edu /medicago.html (1303 words)

	UCSC Genome Browser Home
		The v4.0 whole genome shotgun assembly (Oct. 2004, UCSC fr2) was provided by the US DOE Joint Genome Institute (JGI) as part of the International Fugu Genome Consortium led by the JGI and the Singapore Institute of Molecular and Cell Biology (IMCB).
		We have released a Genome Browser and Blat server for the Feb. 2006 v1.0 draft assembly of Gasterosteus aculeatus produced by the Broad Institute.
		Genome sequence data use restrictions are noted within the species sections on the Credits page.
	genome.ucsc.edu (1212 words)

	Research Abstracts 2000 DOE Human Genome Program
		High resolution whole genome maps can therefore be assembled without library construction and associated cloning artifacts.
		Whole genome maps firstly, enable the size of the genome to be accurately determined, an important prelude to any sequencing endeavor and secondly, provide an in situ picture of the architecture of the entire genome, revealing the number of chromosomes, extrachromosomal elements etc. Populations can be potentially be characterized by comparing maps from different strains.
		Notably, we have constructed a map of the whole human genome at a coverage of 0.6X showing feasibility of complete mapping of the human genome.
	www.ornl.gov /sci/techresources/Human_Genome/publicat/00santa/152.html (524 words)

	Celera: Providing Actionable Diagnostic & Genomic Solutions: Press Release
		This unprecedented genome coverage was achieved using a new system for isolating fragments of DNA for sequencing developed by Celera scientists Hamilton Smith and Robert Holt.
		Celera began to sequence the human genome on September 8, 1999, using the whole genome shotgun technique that its scientists pioneered in sequencing the first complete genome in 1995 at The Institute for Genomic Research (TIGR).
		The human genome sequencing effort funded by governments and the Wellcome Trust is based on sequencing large segments of human DNA in bacterial artificial chromosomes (BAC) using a variation of the shotgun sequencing method.
	www.celera.com /celera/pr_1056581295 (1858 words)

	[No title]
		After Shotgun has been called, other patrons may call "Bitch," "Spanky," or "Comm," referring to the seat behind shotgun, the seat behind the driver, and the center back seat, respectively.
		Quality – The value of an IPSC Shotgun competition is determined by the quality of the challenge presented in the course design.
		Methods using whole genome shotgun data are used to gain a large amount of genome coverage for an organism.
	www.lycos.com /info/shotgun--miscellaneous.html?page=3 (438 words)

	L2TR Genome Sequencing Summary
		Approximately total of 83,000 clones from the whole genome shotgun libraries and BAC clone libraries were sequenced from both ends by dye-terminator using CEQ2000 automated sequencers (Beckman Coulter).
		A total of 102 direct genomic sequences were obtained and assembled, allowing to close 16 gaps and left 6 large contigs.
		Finally, the whole genome assembly was verified by 187 long PCR amplifications (Takara Bio Inc, Japan) of the 15-20 kb fragments throughout the genome with 1kb overlapping.
	www.hawaii.edu /microbiology/MO/L2TRsummary.htm (472 words)

	Whole Genome Shotgun Submissions
		Register your project with the Genome Project database.
		Complete genomes that lack annotation are processed as WGS projects.
		When annotation is added, the complete genome is given a new accession number and the WGS accession number is made secondary, so that Entrez searches for either number will retrieve the complete annotated genome.
	www.ncbi.nlm.nih.gov /Genbank/wgs.html (1629 words)

	Active Skim View of: Whole-Genome Shotgun Sequencing
		When we first started sequencing genomic clones, the biggest limitations were the mathematical tools for putting large numbers of sequences together and the small capacity of the computers available then.
		For the Drosophila genome we had 3 million sequences and for the human genome 45 million sequences, and we only put things together where there was a single mathematical solution.
		The reason the genome is important is that with mass spectroscopy sequencing the proteins get blown apart into small fragments, and we can compare those sequences with the databases.
	www.nap.edu /nap-cgi/skimit.cgi?isbn=0309074363&chap=48-63 (954 words)

	Genomes Pages - At the EBI
		The first completed genomes from viruses, phages and organelles were deposited into the EMBL Database in the early 1980's.
		Since then, molecular biology's shift to obtain the complete sequences of as many genomes as possible combined with major developments in sequencing technology resulted in hundreds of complete genome sequences being added to the database, including Archaea, Bacteria and Eukaryota.
		The Ensembl Genome Browser provides the best possible automatic annotation, graphical views and web-searchable datasets for a number of eukaryotic genomes including human, mouse, drosophila, anopheles, zebrafish with others to follow.
	www.ebi.ac.uk /genomes (389 words)

	Whole-genome shotgun assembly and comparison of human genome assemblies -- Istrail et al. 101 (7): 1916 -- Proceedings ...
		whole-genome shotgun sequencing and assembly of the mouse genome
		Genome Res., January 1, 2005; 15(1): 54 - 66.
		Genome Res., November 1, 2004; 14(11): 2235 - 2244.
	www.pnas.org /cgi/content/full/101/7/1916 (4539 words)

	Tetraodon FAQ
		Whole genome shotgun sequencing is a technique for determining the DNA sequence of a genome by randomly shearing the DNA, sequencing multiple overlapping fragments, and inferring the original sequence from fragments that overlap.
		There are future plans to assemble the Tetraodon shotgun sequence into a whole genome assembly.
		Its mission is to create the tools for genomic medicine and make them freely available to the world and to pioneer their application to the study and treatment of disease.
	www.broad.mit.edu /annotation/tetraodon/faq.html (391 words)

	Rivals dismiss Celera's human genome draft - 05 March 2002 - New Scientist
		They say new analysis reveals the company relied so heavily on publicly-available data that Celera's accomplishment cannot be considered independent, or a victory for their "whole genome shotgun" (WGS) approach to genome sequencing.
		The public effort relied on a strategy where the genome was first broken into large, overlapping pieces, providing a low-resolution map of each chromosome.
		The approach worked for smaller microbial genomes, and seemed successful for relatively simple animal genomes, such as the bacteria and fly.
	www.newscientist.com /article.ns?id=dn1999 (657 words)

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