21. WashU-Zfish Project : Radiation Hybrid (RH) Maps To generate PCR fragments that contain the ends of PAC inserts that can be sequenced. Protocol by B Barbazuk, Washington University Zebrafish genome resources Project, USA. http://www.genetics.wustl.edu/fish_lab/frank/cgi-bin/fish/prot2.html

Home Inverse PCR for PAC-end sequencing Inverse PCR for PAC-end sequencing from Brad Barbazuk Goal is to generate PCR fragments that contain the ends of PAC inserts that can be sequenced. For inverse PCR we cut the PAC once in the vector (near outward primer site) and once at unknown site in insert (and many other places outside these sites, that don't matter). Following ligation to generate small circles, PCR is performed with outward facing primers at the end of the vector that will amplify a product that contains the end of the insert. To increase the odds of getting an amplifiable product, we use two different enzymes (used singly!!) per pac end - NlaIII and RsaI for the SP6 end, and NlaIII and HinPI (or HhaI) for the T7 end. Primers PCYPAC2SP6L GCC GTC GAC ATT TAG GTG PCYPAC2SP6R GAT CGA AAC GGC AGA TCG PCYPAC2T7L CCT TGA GAG CCT TCA ACC PCYOAC2T7R CGA GCT TGA CAT TGT AGG AC Stages in protocol (1) Restriction digest of PAC DNA (2) ligation of restriction digests (3) PCR amplification of ligation products (4) Sequencing of PCR products (5) Trim sequence of primer and vector sequence.

22. Home Contains online genome resources and details of workshops, field trips, courses and educational products, from Cold Spring Harbor, NY. http://www.dnalc.org/

23. National Center For Genome Resources Provides 'MAR-Finder,' A Gene Sequence Anal National Center for genome resources Provides MARFinder, a Gene SequenceAnalysis Tool. A new computer-based gene sequence analysis tool used to identify http://www.ornl.gov/sci/techresources/Human_Genome/archive/articles/marfind.htm

National Center for Genome Resources Provides 'MAR-Finder,' a Gene Sequence Analysis Tool A new computer-based gene sequence analysis tool used to identify DNA regions involved in attachment to the nuclear matrix has been created by a researcher with the National Center for Genome Resources. The tool, called MAR-Finder, is available through the center's Web site at [NCGR URL not available; see http://www.futuresoft.org/MAR-Wiz/ MAR-Finder is among several new Web-based tools developed by the scientific staff at the center to analyze gene sequences or to improve access to the sequences and valuable annotation in NCGR's Genome Sequence DataBase. Scientists in academia and private industry use the database and bioinformatics services provided by NCGR to conduct leading-edge research in genetics, medicine and functional genomics. MAR-Finder, developed by senior computational scientist Gautam B. Singh, uses statistical inference to deduce the presence of matrix association regions, or MARs, in DNA sequences. MARs constitute a significant functional block within sequences and facilitate differential gene expression and DNA replication. MAR-Finder is ideal for researchers interested in DNA structure and identification of genes within a sequence. "MAR-Finder is a valuable tool and its development was a nice meld between a dry and wet lab. You can detect a matrix association region with the computer and test your prediction at the bench that same day," Krawetz said. "And appreciation for the role of MARs in controlling the expression of our genome is growing."

24. ZFIN Genomic Resources Genome and Map Resources; The Danio rerio Sequencing Project at Sanger Zebrafish genome resources at NCBI. cDNA and EST Resources http://zfin.org/zf_info/catch/catch.html

Genomic Resources for Zebrafish (Updated 24 January 2005) Genome and Map Resources The Danio rerio Sequencing Project at Sanger The Sanger zebrafish homepage hosts all of the efforts of the zebrafish genome sequencing project, including the whole genome sequencing and assembly project with automated annotation in Ensembl and the clone mapping and sequencing project with manual annotation in Vega Zebrafish Genome Annotation Browser (Vega) This site allows browsing of zebrafish BAC and PAC clones that were sequenced, analysed and manually annotated within the Sanger zebrafish genome project. Vega includes manually annotated genes with poly A features protein feature and domain annotation Blast searches against all zebrafish ESTs, cDNAs and the WashU and IMCB EST cluster Blast searches against all vertebrate proteins, cDNAs and ESTs mapping of unists markers ab initio gene predictions tRNA prediction CpG island prediction and repeat masking You can search Vega with Blast . For Blast searches against all finished and unfinished clones go here The manual annotation is a joined effort between the Sanger Institute (gene structure annotation) and ZFIN (nomenclature).

25. Genome Resources Human Genome Project. Resources for Education and Exploration Human GenomeProject Information (at Department of Energy) http://www.millerandlevine.com/genome-resources.html

Human Genome Project Resources for Education and Exploration Exploring our Molecular Selves (a genome project education kit) Genetic Education Cente r (University of Kansas) National Human Genome Research Center (at NIH) Human Genome Project Information (at Department of Energy) Human Genome Project Educational resources A Primer on Molecular Genetics Modern Genetics for all Students (from Washington Univ.) Blazing a Genetic Trail (from the Hughes Foundation) The DNA Learning Center (Cold Spring Harbor Lab) DNA from the Beginning (an animated scientific tour) DNA "Chips" (a detailed DNA lab guide for teachers) The Genome News Network (from the Institute for Genomic Research) These resources, from a wide variety of educational institutions and laboratories, provide material that may be useful in the science classroom and laboratory. We particulary recommend "Exploring our Molecular Selves" an education kit that can be ordered from the web (The molecular graphic shown above is taken from this web site)

26. Cold Spring Harbor Laboratory genome resources at Cold Spring Harbor Laboratory The Lita Annenberg HazenGenome Sequencing Center at Cold Spring Harbor performs highthroughput http://www.cshl.org/labs/genome_resources/genome_resources.html

Wednesday, September 21, 2005 CSHL is a research and educational institution. The Laboratory has research programs focusing on cancer, neurobiology, plant genetics, genomics and bioinformatics, and a broad educational mission, including the recently established Watson School of Biological Sciences. Research Staff Cancer Research Plant Genetics Neurobiology ... Library and Archives RNAi Library Search Engine of shRNA constructs from Cold Spring Harbor Laboratory's RNAi library. CSHL Press CSHL Press publishes monographs, technical manuals, handbooks, review volumes, conference proceedings, scholarly journals and videotapes. CSHL's academic program serves to communicate new discoveries, concepts, and methodologies to an international community of scientists. The Watson School of Biological Sciences The Watson School of Biological Sciences offers a novel curriculum that will challenge its graduate students—the biologists of the new millennium—to become leaders in science and in society.

27. The DNA Files - Learn More - Basic Genetics Radio Program General Resources Human Genome Project Laboratory Methods The National Center for genome resources is a nonprofit bioinformatics http://www.dnafiles.org/resources/res01.html

BASIC GENETICS Radio Program General Resources Human Genome Project Genetic Data If you don't know DNA from dodo birds, or if you just need to brush up on your molecular biology, start with General Resources . You'll find everything from an illustrated genetics primer to online dictionaries and glossaries. Scientists announced completing the first draft of the human genome consensus sequence in February 2001. Learn more about this announcement and human genome research from resources listed under Human Genome Project From resources listed under Laboratory Methods , you can learn how scientists go about reading information from tiny, invisible bits of DNA. And if, for whatever reason, you're interested in looking at the human source code itself - strings of As, Ts, Gs, and Cs that scientists have collected so far. Try the Genetic Data links below. Last updated: February 19, 2005 Radio Program The Human Genome Project - Mapping the Future (first distributed in November 1998) Back to Top General Resources Online Dolan DNA Learning Center . Cold Spring Harbor Laboratory The Dolan DNA Learning Center is "the world's first science center devoted entirely to public genetics education." Their highly graphical website includes many interesting educational features, including "

28. World-Wide Web Resources - Human Genome Resources Biology genome resources, compiled by Georgette Howard, UK Pharmacy School . United Kingdom Human Genome Mapping Project Resource Centre http://www.uky.edu/Subject/genome.html

Human Genome Resources , compiled by Georgette Howard, UK Pharmacy School. Gene Map of the Human Genome , shows the chromosome location human genes with links to the underlying sequence and map data. GenLink , is a multimedia database resource. Provides linkage mapping information and software tools that facilitate the integration of physical and genetic linkage data to produce unified maps of the human genome. Genomes Guide: Homo Sapiens Human Genome Research , from US DOE Office of Health and Environmental Research. KEGG: Kyoto Encyclopedia of Genes and Genomes - Numerous genome sequencing projects for different organisms have produced catalogs of genes and related products. Molecular Genetics , from the Max-Plank-Institute for Molecular Genetics. National Center for Genome Resources (US) United Kingdom Human Genome Mapping Project Resource Centre This page was last updated 8 August 2001. To suggest additions or corrections to this list, send mail to Rob Aken, WWW Resources Librarian, at via your browser's mailer or via this form URL: http://www.uky.edu/Subject/genome.html

29. University Of Kentucky Chandler Medical Center Biology genome resources Georgette Howard, Ph.D. Harvard Biological Laboratories.maintains a page of links for Genome Research as well as a comprehensive http://www.uky.edu/Pharmacy/faculty/howard/genome.html

Georgette Howard, Ph.D. Harvard Biological Laboratories maintains a page of links for Genome Research as well as a comprehensive biosciences list of network information resources. Contains a Genome Database (GDB) from the University of Washington Dept. of Pathology , allows one to search GDB by clicking on chromosomal bands in the region of interest. The Center for Genome Research at the Whitehead Institute provides access to their Human and Mouse map releases, software distributions, and software documentation The Jackson Laboratory is the home of genetic and phenotypic databases and the mammalian homology and comparative maps The Cold Spring Harbor Genome WWW page includes information on Genome Topographer and GDB Accessor. See also Cold Spring Harbor Laboratory Information Online. The Portable Dictionary of the Mouse Genome is a compact database of approximately 12,500 loci that you can use on your personal computer. More detailed information can be found in a hypertext guide to the dictionary. The Baylor Genome Center WWW page includes the Biologist's Control Panel , from which you can search biological databases all over the world, browse bibliographic information in France and Italy, access the online catalog at the National Library of Medicine, read the latest copy of Human Genome News , read the bionet newsgroups, and more.

30. Genome Resource Facility - GRF Welcome to the genome resources Facility website at the London School of The Genome Resource Facility (GRF) website is an interactive information centre http://www.lshtm.ac.uk/itd/grf/

The Genome Resource Facility (GRF) website is an interactive information centre relating to the practical use of microarray-based technology and analysis of data generated from microarray experiments. Why has it been created? The GRF has been created as a result of increasing technological developments within the field of genomics and in particular microarrays. Sequencing the genomes of a number of pathogenic microorganisms has allowed staff here at the LSHTM to carry out ground breaking microarray research within this field. The GRF website allows a wealth of information to be easily available for research students, staff and potential collaborators. We hope you find the GRF website useful and if you have any questions regarding microarrays or suggestions to improve the website, please do not hesitate to contact us. Who has created it? The GRF is a departmental initiative founded by Professor Brendan Wren and Dr Nick Dorrell of the Pathogen Molecular Biology Unit at LSHTM. The website authors and designers are Abdi Elmi and Ozan Gundogdu. What are the GRF sections?

31. Human Genome, The Bio-brief. Human Genome Resources And Information Human genome resources and useful information on the human genome project in theUK can be found here. Recently completed, the human genome is thought to be http://www.i-biotechnology.co.uk/human-genome.html

i-bio main menu Biotechnology Genetics Regulatory atlas Genetically modified ... Government regulation human genome Human genome click here for more on the human genome The human genome is one of the most widely publicised and important scientific breakthroughs since the very discovery of DNA in 1953; a genome is the total genetic material in chromosomes, and the drive to complete the human one is an international project between many genetics companies. Exploring the genome Having successfully mapped much of the entire human genome, scientists are now exploring what each gene does in relation to the overall human makeup. The mapping of the human genome continues to be refined, developed and improved upon by genomics companies all over the world, and also the Human Genome Project. Importance The map of the genome provides a unique source of information on how people are "put together", involving structure, function, ability and location of all the individual genes. Genome sequencing technology and useful applications of genomics are constantly improving, and the human genome currently is considered a draft of the final expected result, as scientists refine their search to localising certain genes and traits that may provide beneficial uses in the future. There are roughly 30,000 known genes in the human genome, still far short of the 50,000 to 100,000 originally predicted. click here for more on the human genome top links document.write('<'); document.write('! ');

32. Genome Resources genome resources • ISEQ • Research and Education Center genome resources.• Chicken EST • MPSS Database and Libraries • UD Genome http://ag.udel.edu/research/genomicresources.htm

Research Genome Resources

33. Tetrahymena Genome Data Tetrahymena genome resources. Tetrahymena thermophila Resources at The Institutefor Genomic Research (TIGR). General information about the T. thermophila http://www.ciliate.org/genomedata.shtml

Tetrahymena Genome Database Quick Search: Genome Resources BLAST Textpresso Tetrahymena ... About TGD Tetrahymena Genome Resources Tetrahymena thermophila Resources at The Institute for Genomic Research ( TIGR General information about the T. thermophila Macronuclear Genome Sequencing Project T. thermophila FTP server - Download files containing TIGR's genome sequence assemblies, preliminary gene predictions, and more. T. thermophila Gene Index - Information about genes and EST sequences of T. thermophila TIGR's T. thermophila BLAST server - Search the macronuclear genome assemblies and preliminary gene predictions. TIGR's T. thermophila Genome Annotation Database - Search for preliminary gene annotations through TIGR's MANATEE annotation system. TGD/Other Tetrahymena Resources BLAST at TGD Use WU BLAST 2.0 to search sequences from Tetrahymena and related organisms that are present in international sequence databases (GenBank, EMBL, DDBJ, RefSeq, SwissProt, PIR, PRF, and PDB), including the macronuclear genome sequence determined by TIGR. The protein and DNA sequence datasets searchable at TGD are available via FTP GBrowse at TGD Browse the T. thermophila

34. MaizeGDB External Resources: Non-Plant Genome Resources Useful pages, homepage, BLAST, genome browser, image browser, maize project docs Maize Resources Other Plant Resources NonPlant genome resources http://www.maizegdb.org/links3.php

jobs upcoming events user survey Useful pages homepage BLAST genome browser image browser maize project docs site tour education Maize Newsletter BACs ESTs gene products loci maps metabolic pathways microarrays overgos people/organizations phenotypes probes QTLs references sequences SSRs stocks variations docs reports browse data search ... home Search all records BACs ESTs gene products GO terms locus / loci maps metabolic pathways overgos people/organizations phenotypes probes QTL experiments references sequences SSRs stocks traits variations documents (@ google) i.d. number for MaizeGDB External Resources Non-Plant Genome Resources Maize Resources Other Plant Resources Non-Plant Genome Resources Bioinformatics, Biochemistry, and Metabolic Resources Other Resources Add your own internet resource to MaizeGDB! Bacteria CGSC E. coli Database and Stock Center http://cgsc.biology.yale.edu/ The CGSC Database of E.coli genetic information includes genotypes and reference information for the strains in the CGSC collection, gene names, properties, and linkage map, gene product information, and information on specific mutations. EcoCyc Encyclopedia of E. coli Genes and Metabolism

35. PGRC Home Founded in 1997, the Plant genome resources Center (PGRC) represents a scientificand technological platform for plant genome analysis in barley (Hordeum http://pgrc.ipk-gatersleben.de/

Staff PGRC IPK Modules ... Seminars Founded in 1997, the Plant Genome Resources Center (PGRC) represents a scientific and technological platform for plant genome analysis in barley (Hordeum vulgare) and other crop species. A central unit offers services for automated DNA sequencing and high throughput arraying, developes bioinformatic tools and provides user support in the field of bioinformatics. Complementary to the service core five modules provide expertise and resources in specific target areas. In addition to the establishment of external research collaborations with partners from both the private and the public sector interdepartmental research projects are linked via the PGRC. Most activities of the PGRC are now located in the new genome center that was inaugurated in September 2000. Coordinator: Dr. Patrick Schweizer Tel. +49 (0) 39482-5660 Fax: +49 (0) 39482-5595 email: schweiz@ipk-gatersleben.de

36. Human Genome Resources The following pages are meant to provide a resource of websites, jump to Thesixteen institutions that form the Human Genome Sequencing Consortium http://www.itc.virginia.edu/achs/molbio/software/Human_Genome_resources.html

U.Va. Homepage Help Information Technology and Communication - Academic Computing Health Sciences Human Genome Resources The following pages are meant to provide a resource of web-sites, applications and general information for people wishing to use Human Genome data in their research. please click here to continue... Please send comments/suggestions/questions to Michael Black June 26, 2000: Quoted from the DOE's Joint Genome Institute web page jump to "The sixteen institutions that form the Human Genome Sequencing Consortium include...:" International Human Genome Sequencing Consortium Announces "Working Draft" of Human Genome The Human Genome Project public consortium today announced that it has assembled a working draft of the sequence of the human genome the genetic blueprint for a human being. This major milestone involved two tasks: placing large fragments of DNA in the proper order to cover all of the human chromosomes, and determining the DNA sequence of these fragments. The assembly reported today consists of overlapping fragments covering 97 percent of the human genome, of which sequence has already been assembled for approximately 85 percent of the genome. The sequence has been threaded together into a string of As, Ts, Cs, and Gs arrayed along the length of the human chromosomes.

37. Cichlid Genome Resources Cichlid genome resources. Genetic maps BAC libraries Physical maps cDNAlibraries . The more than 25000 species of bony fishes represent more than http://hcgs.unh.edu/BAC/Tilapia/

Cichlid Genome Resources Genetic maps BAC libraries Physical maps cDNA libraries The more than 25,000 species of bony fishes represent more than half of all living vertebrates. Among these, the perch-like fishes (Order Perciformes) includes more than 9,300 species (Nelson, 1994). We are working with laboratories around the world to develop genomic resources for one of the most diverse groups of Perciformes, the family Cichlidae (>1500 species). Cichlids (pronounced 'siklids') are found in tropical regions of the Americas, Africa, Madagascar and Sri Lanka, but achieve their greatest diversity in the Great Lakes of East Africa. The three major lakes in East Africa (Malawi, Tanganyika and Victoria) each harbor a separate radiation of several hundred species. The radiations in Lakes Malawi and Victoria have occurred in roughly the last million years, making this the most rapid rate of speciation known in vertebrates, and a fascinating system for studying the mechanisms of evolution and speciation. These fishes are also excellent model organisms for studying the genetic and developmental basis for differences in morphology and behavior. Tilapia ( Oreochromis spp.

38. Neurospora As A Model Organism genome resources for Neurospora. The Neurospora crassa genome at the Broad Institute German Neurospora Sequencing Project The Neurospora genome project http://www.fgsc.net/Neurospora/neuros.htm

Genome Resources for Neurospora The Neurospora crassa genome at the Broad Institute German Neurospora Sequencing Project ... The Fungal Genetics Stock Center main page The FGSC holds the strain used at the WICGR (FGSC 9013), the main lab strain, 74-A (FGSC 2489) from which it was derived, the cosmid and BAC libraries used in the US and Germany, as well cDNA libraries used in generating EST data at New Mexico. Contact the FGSC for details 1/7/05 KMC

39. Aspergillus Genome Page Aspergillus genome resources Fungal Genome Resource at the University ofGeorgia Aspergillus genetic maps and locus lists The Aspergillus fumigatus http://www.fgsc.net/aspergenome.htm

Aspergillus genome resources: The Aspergillus genome at the Whitehead Institute Aspergillus genomics web-page (Oklahoma State) ESTs at the University of Oklahoma Fungal Genome Resource at the University of Georgia ... Return to the FGSC main page UPDATED 5/1/03 KMC

40. National Center For Genome Resources BioSpace is globally recognized as the leading provider of webbased resourcesand information to the life science, Biotech and Clinical trial industry. http://www.biospace.com/company_profile.cfm?CompanyID=89504

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