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
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