Laboratory of Beneficial Microbes (Probiotics) for Crops and Sustainable Agriculture Kits (SAKs) for Subsistence Farmers
  • Home
  • Lab Safety
  • Raizada Lab YouTube Videos and Podcasts
  • Latest Lab News
  • Current Projects
  • Manish's Biography
  • Lab Personnel
  • Alumni
  • Books and Publications
  • Press Releases/Media
  • General Public Education: World Hunger
  • Internal
  • Equipment
    • Eqiupment of Interest & Manuals
    • Equipment Inventory
    • Common Use Equipment Inventory
    • Additional Facilities
  • Biologicals - Information for Ontario Grain Farmers
  • Internal FAQs
    • Frequently Asked Questions
  • Lab Having Fun
  • Courses Offered
  • Applicants
    • Prospective Graduate Applicants
    • Prospective Undergrad Applicants
    • Useful Grad Links
    • More About University of Guelph
    • More About City of Guelph
  • Contact Us

Return to Favourite Links

   Molecular Tools

BLAST searching
http://www.ncbi.nlm.nih.gov/BLAST/

I) Molecular Sites with Great Links

Pedro’s BioMolecular Tools
http://www.public.iastate.edu/~pedro/rt_all.html

BioWeb Pasteur
http://bioweb.pasteur.fr

Molecular toolbox at the European Bioinformatics Institute
http://www.ebi.ac.uk/Tools/

NCBI Tools for Data Mining
http://www.ncbi.nlm.nih.gov/Tools/

Genamics SoftwareSeek
http://genamics.com/software/

ChemDex – Directory of Chemistry
http://www.chemdex.org

 II) Specific Molecular Applications

NetPrimer
http://www.premierbiosoft.com/netprimer/netprlaunch/netprlaunch.html
Analyze your PCR primer for hairprin loops or potential dimers that will interfere with PCR: use sense and antisense button to enter in both primers

Primo – PCR Primer design Tools (ChangBiosci)
http://www.changbioscience.com/primo/

PCR Primer Design and Optimization – Excellent Online Lecture
http://www.mcb.uct.ac.za/pcroptim.htm
VectorDesigner Software for creating, labeling, modifying and analyzing vector sequences
https://vectordesigner.invitrogen.com/login.cfm

pDRAW – Free DNA Cloning and Vector Drawing Software (download)
http://www.acaclone.com/

REBASE – Restriction Enzyme Database (take a tour)
http://rebase.neb.com/rebase/rebase.html

Obtain a virtual gel of digested bands from your sequence:
http://rebase.neb.com/rebase/rebtools.html

List of all restriction enzymes (REBASE)
http://rebase.neb.com/rebase/rebase.enz.html

Good online lecture on restriction enzymes
http://escience.ws/b572/L5/L5.htm

Codon Usage Database (very useful when trying to express a transgene)
http://www.kazusa.or.jp/codon/

Index of Plant Chromosome Numbers (Missouri Botanical Gardens)
http://mobot.mobot.org/W3T/Search/ipcn.html

Animal Genome Size Database
http://www.genomesize.com

Plant Genome Size (Cot values) Database (Kew Gardens)
http://www.rbgkew.org.uk/cval/homepage.html

WebElements Periodic Table – to remind yourself of basic chemistry
http://www.webelements.com/

III) Useful Molecular Software Downloads

ProteinExplorer _ free software to view proteins in 3D
http://www.umass.edu/microbio/chime/pe/protexpl/frntdoor.htm

STRAP – Structure Alignment Program for Proteins (free download)
For viewing aligned sequences on 3D protein structure
http://www.charite.de/bioinf/strap/

TreeFinder – to build phylogenetic trees (free download)
http://www.treefinder.de/

ArgusLab – molecular modeling, graphics, drug design (free download)
http://www.planaria-software.com/

CHIME – free molecular visualization
http://www.umass.edu/microbio/chime/

RasMol – molecular visualization freeware (download)
http://www.umass.edu/microbio/rasmol/

Atlas of MacroMolecules – molecular molecules (including DNA, carbohydrates in 3D)
http://www.umass.edu/microbio/chime/atlas/atlas.htm

ChemSketch – freeware to draw chemical structures
http://www.acdlabs.com/download/chemsk.html

Proudly powered by Weebly