Some Useful External Links

If there are any web sites you find useful and visit regularly let us know at the genome lab mailbox.

If you click (regular old left click) on the links below they will open in the existing window. Then you will have to use the Back button to return here.

If you right click on them you will have the option of opening the link in a new window.

Quick Links:

Laboratory recipes Supply sources Online Mol. Biol. tools DNA sequence troubleshooting
Library stuff General seq. databases Specialized seq. databases Modeling/Visualization
Phylogenetic/genotyping software Online Real Time PCR tools

Laboratory recipes and methods

New to PCR?

Small molecule MW calculator	http://www.geocities.com/dsteppan/MWCalc.html
Protein/peptide MW calculator	http://www.mbi.ufl.edu/~shaw/ProtMW2.htm
Nucleic acid calculators below	Jump to them
OpenWetWare.org, a wiki of laboratory information	http://openwetware.org/wiki/Main_Page
Protocol Online	http://www.protocol-online.org/
Laboratory recipes courtesy of the Chin-Sang lab at Queens University	http://130.15.90.245/wormlab_recipe_book.htm
Another selection of methods and protocols links	http://www.cellbio.com/protocols.html
BioTechniques Molecular Biology Forum	http://molecularbiology.forums.biotechniques.com/forums/index.php
Buffer recipe collection	http://www.thelabrat.com/protocols/reagents.shtml
Cool online buffer calculator	http://www.liv.ac.uk/buffers/buffercalc.html
On the chemistry of buffer preparation	http://www.haverford.edu/chem/Scarrow/GenChem/acidbase...
Agarose gels basic how-to	http://www.methodbook.net/dna/agarogel.html http://openwetware.org/wiki/Knight:Agarose_gel_electrophoresis
"PCR Jumpstation" - good background and how-to info	http://www.horizonpress.com/gateway/pcr.html
"PCR Additives" - what are those magical substances?	http://www.staff.uni-mainz.de/lieb/additiva.html

Some commonly requested reagent and supply sources

UW Chemistry Stockroom	http://depts.washington.edu/chem/facilserv/stockroom.html
UW Biochemistry Stores	http://depts.washington.edu/biowww/stores/index.html
Better Buffer and other clever reagents.	http://www.gelcompany.com
MapMarker size standards and other clever reagents.	http://www.bioventures.com
Inexpensive Taq and other stuff.	http://www.genscript.com
Matrix pipettes/tips	http://www.matrixtechcorp.com/handheld/tips.aspx?id=37

Online General Molecular Biology Tools

Primer 3.0	http://frodo.wi.mit.edu/cgi-bin/primer3/primer3.cgi
The PCR Suite - works with Primer 3.0	http://www2.eur.nl/fgg/kgen/primer/index.html
IDT's Oligo Analyzer 3.0	http://www.idtdna.com/analyzer/Applications/OligoAnalyzer...
Oligo calculator, for DNA and RNA	http://www.justbio.com/oligocalc/index.php
Another one	http://www.protocol-online.org/cgi-bin/prot/view_cache.cgi?ID...
Find primers from gene sequence data	http://seq.yeastgenome.org/cgi-bin/web-primer
Java based PCR optimization tool	http://www.molbiol.ru/eng/scripts/01_14.html
A comprehensive collection of PCR primer design tools	http://www.changbioscience.com/primo/

Fluorescent DNA sequencing - troubleshooting resources

A troubleshooting guide	http://www.nucleics.com/DNA_sequencing_support/DNA-seq....
Nicely illustrated sequence result examples at the OSU core lab	http://corelabs.cgrb.oregonstate.edu/sequence/troubleshoot
Good list of bad contaminants	http://www.science.mcmaster.ca/mobixlab/sequencing/seqtroubles...
The ABRF* has the most comprehensive list imaginable of what can go wrong	http://www.abrf.org/index.cfm/stwr.home
A site with reviews of sequencing services and tips	http://www.molecular-biology.org/

* Association of Biomolecular Research Facilities

Library Stuff

General Sequence databases

Specialized sequence databases

Modeling & Visualization


Pub Med	http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed
UW site-licensed software, etc., (HealthLinks page)	http://healthlinks.washington.edu/index.jsp?id=dcf7....
UW library Reference Tools	http://www.lib.washington.edu/research/
UW library E-Journals Search	http://www.lib.washington.edu/types/ejournals/
NCBI Entrez DNA Sequences	http://www.ncbi.nlm.nih.gov/sites/entrez?db=Nucleotide
EMBL DNA sequence databank	http://www.ebi.ac.uk/embl/
Japanese DNA sequence databank	http://www.ddbj.nig.ac.jp/
NCBI Entrez Genomes	http://www.ncbi.nlm.nih.gov/sites/entrez?db=Genome
GENSCAN server	http://genes.mit.edu/GENSCAN.html
NCBI Entrez Protein Sequences	http://www.ncbi.nlm.nih.gov/sites/entrez?db=protein
Protien Information Resource	http://pir.georgetown.edu/
Swiss-Prot knowledgebase	http://ca.expasy.org/sprot/sprot-top.html
Japanese cloning vector database	http://www.shigen.nig.ac.jp/cvector/cvector.html
Netherlands Academy of Arts and Sciences database with cloning vectors	http://www.cbs.knaw.nl/databases/
Plasmid databank	http://www.geocities.com/HotSprings/Spa/3013/plasmid.html
NEB restriction enzyme database	http://rebase.neb.com/rebase/rebase.html
Codon usage database	http://www.kazusa.or.jp/codon/
NCBI EST database search	http://www.ncbi.nlm.nih.gov/dbEST/index.html
GeneNest database	http://genenest.molgen.mpg.de/
Molecular modeling tools center	http://mmtsb.scripps.edu/
Simple calculators to protein molecular motion displays	http://www.martindalecenter.com/Calculators3_2_Bio.html

Phylogenetic and Genotyping Software

Phylogeny programs, cross-referenced by method and system	http://evolution.genetics.washington.edu/phylip/software.html
Phylip	http://evolution.gs.washington.edu/phylip.html http://www.sinauer.com/detail.php?id=8060
Mr. Bayes	http://mrbayes.csit.fsu.edu/
AFLPapp	http://hordeum.msu.montana.edu/software/AFLPapp/software.html
Genographer	http://hordeum.msu.montana.edu/software/genographer/
GeneMarker	http://www.softgenetics.com/GeneMarker.html


SnP fact sheet	http://www.ornl.gov/sci/techresources/Human_Genome/faq/snps...
Fragment analysis experimental design considerations	http://awcmee.massey.ac.nz/genome-genotyping-experimental-des...

Online Real Time PCR tools

Real Time PCR Tutorial	http://pathmicro.med.sc.edu/pcr/realtime-home.htm
BioSearch's Real Time PCR assay design software	http://www.biosearchtechnologies.com/products/probe_design.asp...
Genscript's TaqMan primer design tool	https://www.genscript.com/ssl-bin/app/primer
Some TaqMan primer design guidelines	http://keck.med.yale.edu/affymetrix/rtpcr/design.htm
Big Q-PCR primer databank at the NCI based on PubMed	http://web.ncifcrf.gov/rtp/gel/primerdb/
Collection of validated primer sets for Q-PCR	http://www.realtimeprimers.org/
Another big Q-PCR primer databank	http://pga.mgh.harvard.edu/primerbank/index.html
Primer databank based on researcher submissions	http://medgen.ugent.be/rtprimerdb/