Links and Tools


The links below are commonly used external tools for exploration of molecular biology and protein chemistry.

Miscellaneous Molecular Biology Tools:

1)    Primer3- http://frodo.wi.mit.edu/primer3
2)    NCBI Blast: http://blast.ncbi.nlm.nih.gov/Blast.cgi
3)    Protein translation: http://web.expasy.org/translate
4)    Tool for electroporation of multiple plasmids: http://www.gabyhaddock.com/electroporator
5)    NEB Double Digest: http://www.neb.com/nebecomm/DoubleDigestCalculator.asp
6)    NEB Cutter: http://tools.neb.com/NEBcutter2/index.php
7)    Ambion’s siRNA Target Finder: http://www.ambion.com/techlib/misc/siRNA_finder.html

In situ/gene expression databases:

1)    Gensat project: http://www.ncbi.nlm.nih.gov/projects/gensat
2)    St Jude’s BGEM: http://www.stjudebgem.org/web/mainPage/mainPage.php
3)    Allen Brain Atlas: http://mouse.brain-map.or/welcome.do;jsessionid=8951F0FCE082DE583F1B0FB11B462FAD
4)    Zebrafish: http://zfin.org/cgi-bin/webdriver?MIval=aa-xpatview.apg&OID=ZDB-GENE-031105-1
5)    Northern expression: http://biogps.gnf.org/#goto=genereport&id=12934
6)    Genepaint: http://www.genepaint.org/Frameset.html

Gene information:

1)    Gene Network for navigating the literature: http://www.ihop-net.org/UniPub/iHOP
2)    Entrez Gene: http://www.ncbi.nlm.nih.gov/gene
3)    Next Bio (Drug targets): http://www.nextbio.com/b/search/ov/Dpysl2?id=282608&type=feature

Protein information:

1)    Master page: http://expasy.org
2)    Protein Knowledge database: http://www.uniprot.org

Transgenic mice:

1)    Mutant Mouse Regional Resources: http://www.mmrrc.org/
2)    The Jackson Labs: http://www.jax.org
3)    Taconic Labs: http://www.taconic.com/wmspage.cfm?parm1=31
4)    Charles Rivers: http://www.criver.com/en-us/ProdServ/ByType/ResModOver/Pages/home2.aspx
5)    Komp (archive of NIH knockouts in ES cells): https://www.komp.org

Protein interactions:

1)    Int-act: http://www.ebi.ac.uk/intact/main.xhtml
2)    MINT:  http://mint.bio.uniroma2.it/mint/search/searchWelcome.do?queryType=protein
3)    http://www.thebiogrid.org/index.php

 
Finding Antibodies:

1)    Exact Antigen:http://www.labome.com

Pathway analysis:

1)    Kegg Pathways in flies: http://www.genome.jp/kegg-bin/get_htext?query=04360&htext=br08901.keg
2)    Reactome – biological pathways: http://www.reactome.org/ReactomeGWT/entrypoint.htm1