Van Oudenaarden Lab:Internal

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Reagents list
Restriction enzymes (-20C fridge)
Chores list

Books in the lab



Online tools:

NebCutter V2.0 Restriction and other DNA analysis, with great GUI.
Primer3 Primer design tool best for creating compatible primer pairs for a given template.
Netprimer Primer test tool. Verify melting temperatures, hairpins, dimerization, &c of final primer designs.
NCBI National Center for Biotechnology Information
Entrez Biology search engine, e.g. for looking up protein and DNA sequences by name
PubMed Literature search
BLAST Basic Local Alignment Search Tool, for DNA/protein alignment and comparison, primer verification, etc.
Google Scholar Most general literature search tool.

Freeware:
WinGene Tool for analyzing nucleotide sequences. Best for reverse complements and primer checks.
MFI For converting flow cytometer output files to ASCII. Simple free registration.
OpenOffice.org Open source office environment, fully compatible (well, almost) with MS Office, including Powerpoint.
Open Perl IDE Open source Integrated Development environment for Perl. Easy to set up and use.
ActivePerl Easy installation for running Perl scripts in Windows; necessary for Open Perl IDE.

Perl scripts:
deannotate_dna.pl A useful script for annotating and editing DNA sequences. This file provides documentation and an example.
cytometry.zip Package of scripts and executables for quickly processing raw flow cytometer files into a table of histograms. Consult Michael on its use.


Protocols:
General
E. Coli
Yeast
Cyanobacteria


additions, corrections, &c: <mokelly@mit.edu>
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