Websites for Principles of Gene Manipulation

The Internet provides a vast resource for the biologist interested in gene manipulation because it links all research laboratories, biotechnology companies, government organizations, publishers and suppliers allowing instant access to up-to-the-minute information. We list below a selection of websites that are particularly useful or relevant to the various chapters of Principles of Gene Manipulation. A number of gateway sites are listed first, as these provide general biology resources and a large number of links.

1. Gateway sites
General gateway sites, or 'jumpstations' with links to a variety of molecular biology resources
http://www.highveld.com/molbiol.html
http://www.unl.edu/stc-95/ResTools/cmshp.html http://www.horizonpress.com/gateway/iftmb.html

>back to top<

2. Basic techniques
http://www.protocol-online.net/molbio/basic/basic.htm
A very useful site with detailed background discussion of principles and applications of many of the techniques discussed in the earlier part of the book

http://www.protocol-online.net/molbio/PCR/standard_pcr.htm http://www.highveld.com/pcr.html
The first site covers many of the PCR-based techniques which are covered in the book. Many other resources for PCR can be found in the second site.

>back to top<

3. Vectors and cloning
Several databases for cloning vectors have been set up but these are generally limited in the information they provide. The best sources of information on cloning vectors are the biotechnology companies, which also provide enzymes, other reagents and molecular biology kits. Commercial websites for selected companies are listed below:

http://www.ambion.com/
http://www.neb.com/
http://www.lifetech.com/
http://www.stratagene.com/
http://www.clontech.com/index.shtml
http://www.promega.com

In addition, the following comprehensive databases maintained by New England Biolabs provide up-to-date information on restriction enzymes and inteins

http://rebase.neb.com/rebase/rebase.html http://www.neb.com/neb/inteins.html intein database

A gateway site to virology on the Internet, including information on specific viruses and their development as vectors for gene transfer to plants, animal cells and in gene therapy applications can be found on the following site: http://www.tulane.edu/~dmsander/garryfavweb.html

>back to top<

4. Sequencing and bioinformatics
A large number of Internet resources exist for sequencing, sequence analysis and bioinformatics tools. Many of these are outside the scope of Principles of Gene Manipulation, and will be discussed in more detail in our forthcoming sister site for Principles of Genome Analysis. We restrict the list below to gateways, general sequence depositories and the most commonly used sequence analysis tools.

The following sites are commonly used gateways to a variety of sequence analysis and bioinformatics resources: National Center for Biotechnology Information (NCBI): http://www.ncbi.nlm.nih.gov
The Sanger Centre: http://www.sanger.ac.uk
EBI-European Bioinformatics Institute (EMBL): http://www.ebi.ac.uk

General sequence repositories
http://www.ddbj.nig.ac.jp/
http://www.ebi.ac.uk/embl/
http://www.ncbi.nlm.nih.gov

Collections of non-redundant gene sequences based on gene and EST sequences
http://www.ncbi.nlm.nih.gov/UniGene/
http://www.tigr.org/tdb/tgi.shtml

Bioinformatics tools for sequence analysis
BLAST: http://www.ncbi.nlm.nih.gov/BLAST
FASTA: http://fasta.bioch.virginia.edu

>back to top<

5. Cloning in other species
The second half of principles of gene manipulation is devoted to cloning in species other than E. coli, including other bacteria, yeast, animals and plants. In the current era of genome projects, a large number of organism-specific databases have been set up, which provide comprehensive resources for these organisms including sequencing and functional genomics projects which involve many of the procedures described in the book. There are also sites devoted to specific transgenic technologies. Some of these are also listed below.

General genome databases providing information on sequencing projects and links to specific organisms

http://www.unl.edu/stc-95/ResTools/biotools/biotools10.html http://www.tigr.org/tdb/mdb/mdbcomplete.html http://igweb.integratedgenomics.com/GOLD/

There are also a number of organelle genome databases: http://megasun.bch.umontreal.ca/gobase/gobase.html
http://bio-www.ba.cnr.it:8000/BioWWW/#AMMTDB http://www3.ebi.ac.uk/Research/Mitbase/mitbase.pl

Resources for specific organisms. Again, a more comprehensive list is provided on out sister site. The organisms represented here are those featured most frequently in PRINCIPLES OF GENE MANIPULATION.

General resources for E. coli, B. subtilis and Streptomyces:
EcoWEB: http://bmb.med.miami.edu/EcoGene/EcoWeb/ List of sites related to E. coli: http://genolist.pasteur.fr/Colibri/help/others.html Non-Redundant B.subtilis database: http://pbil.univ-lyon1.fr/nrsub/nrsub.html SubtiList WWW server: http://genolist.pasteur.fr/SubtiList/ Streptomyces resources at the Sanger Centre and John Innes Centre: http://www.sanger.ac.uk/Projects/S_coelicolor/ http://www.jic.bbsrc.ac.uk/science/molmicro/Strept.html

Resources for yeast: Saccharomyces genome database:
http://genome-www.stanford.edu/Saccharomyces/ Further resources for Saccharomyces, Schizzosaccharomyces and Candida are listed at: http://genome-www.stanford.edu/Saccharomyces/yeast_info.html

http://www.acedb.org/ A database developed initially for the nematode worm C. elegans, and recently expanded to include information on yeast and humans. Other C. elegans resources include WORMbase: http://www.wormbase.org/ and the C. elegans WWW server: http://elegans.swmed.edu/

http://flybase.bio.indiana.edu/ A comprehensive Drosophila resource including genomic data and information on transgenic and mutant fly strains. Other useful Drosophila resources include the Interactive Fly: http://sdb.bio.purdue.edu/fly/aimain/1aahome.htm and FlyView: http://pbio07.uni-muenster.de/Home.html, which provides thousands of pictures of enhancer trap lines.

Genome resources for the mouse include: http://www.informatics.jax.org/

There are also a number of sites devoted to transgenic mouse strains, mouse gene knockouts and gene trap insertions -

The Jackson laboratory website, describing over 2,500 strains of targeted mutant mice: http://jaxmice.jax.org/index.shtml TBASE, a comprehensive transgenic and targeted mutant database run by the Jackson laboratory: http://tbase.jax.org. Frontiers in Science gene knockout database: http://www.bioscience.org/knockout/knochome.htm BioMedNet Mouse Knockout Database: http://biomednet.com/db/mkmd Databases for Cre transgenic mice and floxed mouse genes: http://www.mshri.on.ca/nagy/cre.htm Database of gene trap insertions: http://socrates.berkeley.edu/~skarnes/resource.html

Human genome resources include: Online Mendelian Inheritance in Man: http://www3.ncbi.nlm.nih.gov/Omim/ The human genome database: http://www.gdb.org/ GenLink: http://www.genlink.wustl.edu/

The XenBase site provides a comprehensive resource for Xenopus genetics including gene transfer technology and transgenic strains: http://www.xenbase.org/Xenbase.html

The following sites provide resources for plant genome projects, mutant and transgenic plants:

Arabidopsis thaliana:
The Arabidopsis Information Resource (TAIR): http://www.arabidopsis.org/ Institute for Genomic Research Arabidopsis resource: http://www.tigr.org/tdb/e2k1/ath1/
Gateway to resources for many crop plants: http://ukcrop.net/ Maize genome project: http://zmdb.iastate.edu/
Rice genome project: http://www.tigr.org/tdb/e2k1/osa1/

>back to top<