
	Where results make sense

Topic: Genome assembly

	IMCB - FUGU Genome Project
		Fugu genome is among the smallest vertebrate genomes and has proved to be a valuable ‘reference’ genome for identifying genes and other functional elements such as regulatory elements in the human and other vertebrate genomes, and for understanding the structure and evolution of vertebrate genomes.
		Fourth Fugu Genome assembly (October 2004; v4) This assembly is based on ~8.7X coverage of the genome, and includes 7,213 scaffolds, constituting 393 Mb of the genome.
		90% of the genome is represented on 1118 scaffolds.
	www.fugu-sg.org (355 words)

	[No title]
		For instance, the mouse genome is assembled by an external group and annotated via the NCBI annotation pipeline.
		Genomic contigs are constructed in two steps: a clone layout stage, followed by a sequence building stage.
		A first set of known genes (and their corresponding transcripts and proteins) are identified by aligning reference sequences (RefSeq) to the assembled genomic sequence using MegaBLAST (1) and assembling the hits according to limited constraints and heuristics regarding exon structure.
	www.ncbi.nlm.nih.gov /genome/guide/build.html (2666 words)

	UT Genome Browser
		Assembly: This new revision whole genome shotgun assembly was constructed with the RAMEN assembler as before, based on ~9X coverage of the genome with additional data including BAC and fosmid end-pairs.
		Since the current version is still a preliminary one and may contain mistakes, users should use the data at their own risk and are not allowed to redistribute or repackage the data.
		Members in the UT Genome Browser Development Team are grateful to Kiyoshi Naruse, Daisuke Kobayashi, and Takanori Narita for their valuable input to improve the functions of the browser in a variety of ways.
	medaka.utgenome.org (748 words)

	AMOS - A Modular Open-Source Assembler
		These assembly objects can be written to and read from a central data repository, allowing for separate modules to build on and improve existing assemblies in discrete steps.
		Such utilities include a tool for comparing two distinct assemblies, a tool for comparing an assembly to a reference genome, and a tool for identifying potential errors in the assembly by examining the mate-pair layout and polymorphisms in the assemblies.
		Sequences that match the finished genome at 90% identity for over 80% of their trimmed length (as aligned by MUMmer) are included in the matching set, while all other reads are grouped into the non-matching set.
	amos.sourceforge.net (2428 words)

	GENE PREDICTIONS on GENOMES
		These are the predictions for the Feb.2004 version of the chicken genome assembly produced at the Genome Sequencing Center at Washington University in St. Louis.
		These are the predictions for the Nov. 13 2003 version of the ARACHNE assembly of the chimpanzee genome, produced by the Chimpanzee Sequencing Consortium.chicken genome assembly produced at the Genome Sequencing Center at Washington University in St. Louis.
		Version of the genome: goldenPath assembly Apr. 2005 freeze of the D. simulans genome (droSim1) from the Genome Sequencing Center at Washington University School of Medicine in St. Louis.
	www1.imim.es /genepredictions (2580 words)

	GSC - SARS-associated Coronavirus (Site not responding. Last check: 2007-10-17)
		The Genome Sciences Centre SARS associated virus genome sequencing project is collaboration with the British Columbia Centre for Disease Control and the National Microbiology Laboratory, Winnipeg.
		Genome Sciences Centre in partnership to sequence the SARS virus genome...more
		The Genome Sciences Centre carries a wide range of basic and applied research in genomics, including sequencing, physical mapping, functional genomics, cancer genomics, gene expression and technology development.
	www.bcgsc.ca /bioinfo/SARS (675 words)

	UCSC Genome Browser: User's Guide
		Assembly errors and sequence gaps may still occur well into the sequencing process due to regions that are intrinsically difficult to sequence.
		During the conversion process, portions of the genome in the coordinate range of the original assembly are aligned to the new assembly while preserving their order and orientation.
		Genomic sequence reads from 3 alternate strains of chicken (Broiler, Layer and Silkie) were used to determine the SNPs relative to the reference assembly for the Red Jungle Fowl (RJF).
	mgc.ucsc.edu /goldenPath/help/hgTracksHelp.html (15456 words)

	Celera Genomics: 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.
		The second assembly method used by Celera is its “Regional Assembler.” This is being used to cross validate the results from the whole genome shotgun assembly.
		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 (1849 words)

	[Genome] mis-assembly (Site not responding. Last check: 2007-10-17)
		Graem it may or may not be possible to correct this in the next mouse assembly.
		It is the sort of thing almost certain to fall out of the wash as we slowly transition from the whole genome shotgun to a finished bac-by-bac approach.
		I notice that there are some assembly gaps close to the crybb1 fragment that is on chr5.
	www.cse.ucsc.edu /pipermail/genome/2002-October/001388.html (359 words)

	Analysis of Segmental Duplications and Genome Assembly in the Mouse -- Bailey et al. 14 (5): 789 -- Genome Research
		Both the human and mouse genomes have alignments at all levels of identity; however, the human genome has a dramatically greater amount of aligned bases relative to the mouse (227,812 kbp vs. 10,042 kbp).
		DeBerardinis, R.J., Goodier, J.L., Ostertag, E.M., and Kazazian Jr., H.H. Rapid amplification of a retrotransposon subfamily is evolving the mouse genome.
		Genomic inversions of human chromosome 15q11-q13 in mothers of Angelman syndrome patients with class II (BP2/3) deletions.
	www.genome.org /cgi/content/full/14/5/789 (6552 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 (4336 words)

	The Atlas Genome Assembly System -- Havlak et al. 14 (4): 721 -- Genome Research
		The actual trimming of the rat genome reads used a window size of 50, a minimum boundary quality of 20, and also imposed other requirements on passing windows and regions.
		The genome sequence of the malaria mosquito Anopheles gambiae.
		Genome Res., January 1, 2005; 15(1): 1 - 18.
	www.genome.org /cgi/content/full/14/4/721 (7633 words)

	PCAP Genome Assembly Program and CAP3 Sequence Assembly Program (Site not responding. Last check: 2007-10-17)
		The assembly was produced on an SGI Altix with 30 GB of main memory and 16 processors of 900 MHz.
		The assembly was performed with the PCAP program (Parallel Contig Assembly Program) on a cluster of Compaq ES40 servers.
		The assembly used the December release of the public whole genome shotgun data from NCBI.
	seq.cs.iastate.edu (331 words)

	[Genome] mis-assembly (Site not responding. Last check: 2007-10-17)
		It is the sort of thing almost > certain to fall out of the wash as we slowly transition > from the whole genome shotgun to a finished bac-by-bac > approach.
		> > I notice that there are some assembly gaps close to the crybb1 fragment that > is on chr5.
		It should be linked head to head with the crybA4 gene on chr 5.
	www.cse.ucsc.edu /pipermail/genome/2002-October/001389.html (384 words)

	Arachne: A Whole Genome Assembly Software Package
		Arachne is a tool for assembling genome sequences from whole genome shotgun reads, mostly in forward-reverse pairs obtained by sequencing clone ends.
		Base calls and quality scores are provided for each contig, along with the approximate locations of the reads which were used to build it.
		Many of Arachne's algorithms are described in "ARACHNE: A Whole-Genome Shotgun Assembler", Genome Research, January 2002, and "Whole-Genome Sequence Assembly for Mammalian Genomes: ARACHNE 2", Genome Research, January 2003.
	www.broad.mit.edu /wga (179 words)

	UCSC Genome Browser: Downloads
		The latest version of the UCSC Genome Browser source code may be downloaded here.
		Prior to downloading or using the Genome Browser source, please review the source code licensing requirements.
		All of the tables in the Genome Browser are freely usable for any purpose except as indicated in the README.txt files in the download directories.
	hgdownload.cse.ucsc.edu /downloads.html (824 words)

	NCBI Human Genome Resources
		A challenge facing researchers today is that of piecing together and analyzing the plethora of data currently being generated through the Human Genome Project and scores of smaller projects.
		NCBI's Web site serves an an integrated, one-stop, genomic information infrastructure for biomedical researchers from around the world so that they may use these data in their research efforts.
		Spectral karyotyping and comparative genome hybridization data for studying chromosome abnormalities.
	www.ncbi.nlm.nih.gov /projects/genome/guide/human (459 words)

	Mouse (Mus musculus)
		Entries have been added to the assembly so that BAC clones can be fetched.
		Ensembl Mouse is based on the NCBI m34 mouse assembly (freeze May 17, 2005, strain C57BL/6J).
		The Mouse Genome Sequencing Consortium is a joint project between The Whitehead Institute/MIT Center for Genome Research, The Washington University Genome Sequencing Center, The Wellcome Trust Sanger Institute and EMBL - EBI to provide the Mouse genome sequence to the world.
	www.ensembl.org /Mus_musculus (295 words)

	Rat - Genome Assembly (Site not responding. Last check: 2007-10-17)
		Rat City Rollergirls - Seattle roller derby league.
		The HGSC is sequencing the genome of the rat (Rattus norvegicus).
		The Rat Genome Sequencing Consortium is led by the Baylor College of Medicine Human
	publicdot.com /pd/rat.html (192 words)

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