note:
Go to the Bioinformatics section to find out about how to use the
programs of the links below!DNA sequence analysis:
EMBOSS (http://emboss.bioinformatics.nl/)
ApE (download from
http://biologylabs.utah.edu/jorgensen/wayned/ape/)
First save the zip file, open it, and only then run the ApE.exe!
An
on-line calculation form for the
Tm of PCR primers
according to the so-called Nearest Neighbour methode
can be found at:
http://www.basic.northwestern.edu/biotools/oligocalc.html
For alignment of two given sequences:
Go to
(https://blast.ncbi.nlm.nih.gov/Blast.cgi
)
Click on the Nucleotide BLAST picture.
In the Enter Query Sequence section, check the option Align two or more sequences.
Fill-in your two sequences, and click the BLAST button.
To find all open reading frames (ORFs) in a given sequence:
ORF Finder (https://www.ncbi.nlm.nih.gov/orffinder/
)
Other links:
http://www.bioinformatics.nl/molbi/SCLIntro is a perfect start to
find out about activities in the GeneTech practicals.
The REbase
site (
http://rebase.neb.com/rebase/rebase.html ) is a comprehensive
source of information about restriction enzymes.
SCL Questions links:
Wet Lab examples:
How to read a long run vector & donor digestion photo:
http://www.bioinformatics.nl/molbi/SCLexamples/DigGel/
How to read a group B miniprep gel photo:
http://www.bioinformatics.nl/molbi/SCLexamples/BgroupMpGel/
How to read a group A miniprep gel photo:
http://www.bioinformatics.nl/molbi/SCLexamples/AgroupMpGel/
How to read a group A first PCR gel photo:
http://www.bioinformatics.nl/molbi/SCLexamples/AgroupsPCRgel1/
How to read a group A second PCR gel photo:
http://www.bioinformatics.nl/molbi/SCLexamples/AgroupsPCRgel2/
How to read a group B gel-purified fragments gel photo:
http://www.bioinformatics.nl/molbi/SCLexamples/BgroupsFragsGel/
Lin's hybridisation blot signal from PCR probes
http://www.bioinformatics.nl/molbi/SCLexamples/LinsHybrSignals_grA
Lin's hybridisation blot signal from gel-purified probes
http://www.bioinformatics.nl/molbi/SCLexamples/LinsHybrSignals_grB
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