Single DNA Sequence Analysis Tools. BME 110: CompBio Tools Todd Lowe May 6, 2008. Today’s topics. ORF prediction Restriction enzyme search tools PCR primer design Using on-line tools from ExPASy. Basic ORF Finding. Look for “long” open reading frames
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BME 110: CompBio Tools
May 6, 2008
Nla III: 5’ ... CATG^ ... 3’
BamH I: 5’ ... G^GATCC... 3’
Dra III: 5’ ... CACNNN^GTG... 3’
> 3,000 RE’s found to date with >200 specificities!
5’-ATTGATGG^AATTCTTATGGATAG-3' 3'- 3’-TAACTACCTTAA^GAATACCTATC-5'
After cutting, “sticky ends”:
3’-TAACTACCTTAA + GAATACCTATC-5‘
Same DNA cut by different restriction enzymes give different fragment lengths
NEBcutter – Display which restriction enzyme cut in your sequence, and where
REBsites – Display a “virtual” digest of your DNA, showing how it would look on an agarose gel
(Rest are usually OK as defaults)
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