Van Oudenaarden Lab:Internal

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<br /> Reagents list<br />[[Van_Oudenaarden_Lab:Enzymes | Restriction enzymes]] (-20C fridge)<br /> Chores list<br/>
<br /> Reagents list<br />[[Van_Oudenaarden_Lab:Enzymes | Restriction enzymes]] (-20C fridge)<br /> Chores list<br/>
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[[Van_Oudenaarden_Lab:Books | Books in the lab]]<br />[[Van_Oudenaarden_Lab:ImProToo | Image Processing Tools ]]
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[[Van_Oudenaarden_Lab:Books | Books in the lab]]<br />[[Van_Oudenaarden_Lab:Image Processing | Image Processing Tools ]]
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<span style="font-style: italic;"><big><span style="font-weight: bold;"></span></big>Online tools:</span><br /><div style="margin-left: 40px;">[http://tools.neb.com/NEBcutter2/index.php <span style="font-weight: bold;"><big><span style="font-weight: bold;"></span></big></span>]<span style="font-family: times new roman,times,serif;">[http://tools.neb.com/NEBcutter2/index.php NebCutter V2.0] Restriction and other DNA analysis, with great GUI.<br />[http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www.cgi Primer3] Primer design tool best for creating compatible primer pairs for a given template. <br />[http://www.premierbiosoft.com/netprimer/netprlaunch/netprlaunch.html Netprimer] Primer test tool. Verify melting temperatures, hairpins, dimerization, &c of final primer designs. <br /> </span> <span style="font-family: times new roman,times,serif;"> [http://www.ncbi.nlm.nih.gov/ NCBI] National Center for Biotechnology Information</span><br /><span style="font-family: times new roman,times,serif;"> </span><div style="margin-left: 40px;">[http://www.ncbi.nlm.nih.gov/Entrez/index.html Entrez] Biology search engine, e.g. for looking up protein and DNA sequences by name<br />[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed PubMed] Literature search<br />[http://www.ncbi.nlm.nih.gov/BLAST/ BLAST] Basic Local Alignment Search Tool, for DNA/protein alignment and comparison, primer verification, etc.<br /> </div> </div><div style="margin-left: 40px;">[http://scholar.google.com/ Google Scholar] Most general literature search tool. <br /><br /> </div><span style="font-style: italic;">Freeware:</span><br /><div style="margin-left: 40px;">[http://www.ipw.agrl.ethz.ch/%7Elhennig/wingene.html WinGene] Tool for analyzing nucleotide sequences. Best for reverse complements and primer checks.<br />[http://www.umass.edu/microbio/mfi/ MFI] For converting flow cytometer output files to ASCII. Simple free registration. <br />[http://www.openoffice.org/ OpenOffice.org] Open source office environment, fully compatible (well, almost) with MS Office, including Powerpoint.<br />[http://open-perl-ide.sourceforge.net/ Open Perl IDE] Open source Integrated Development environment for Perl. Easy to set up and use.<br />[http://www.activestate.com/Products/ActivePerl/?_x=1 ActivePerl] Easy installation for running Perl scripts in Windows; necessary for Open Perl IDE. <br /><br /> </div><span style="font-style: italic;">Perl scripts:<br /> </span><div style="margin-left: 40px;">[http://www.mit.edu/~mokelly/avo/deannotate_dna.pl deannotate_dna.pl] A useful script for annotating and editing DNA sequences. [http://www.mit.edu/~mokelly/avo/annotation%20documentation.txt This file] provides documentation and an example.<br />[http://www.mit.edu/~mokelly/avo/cytometry.zip cytometry.zip] Package of scripts and executables for quickly processing raw flow cytometer files into a table of histograms. Consult Michael on its use. <br /> </div><div style="margin-left: 40px;"> </div>
<span style="font-style: italic;"><big><span style="font-weight: bold;"></span></big>Online tools:</span><br /><div style="margin-left: 40px;">[http://tools.neb.com/NEBcutter2/index.php <span style="font-weight: bold;"><big><span style="font-weight: bold;"></span></big></span>]<span style="font-family: times new roman,times,serif;">[http://tools.neb.com/NEBcutter2/index.php NebCutter V2.0] Restriction and other DNA analysis, with great GUI.<br />[http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www.cgi Primer3] Primer design tool best for creating compatible primer pairs for a given template. <br />[http://www.premierbiosoft.com/netprimer/netprlaunch/netprlaunch.html Netprimer] Primer test tool. Verify melting temperatures, hairpins, dimerization, &c of final primer designs. <br /> </span> <span style="font-family: times new roman,times,serif;"> [http://www.ncbi.nlm.nih.gov/ NCBI] National Center for Biotechnology Information</span><br /><span style="font-family: times new roman,times,serif;"> </span><div style="margin-left: 40px;">[http://www.ncbi.nlm.nih.gov/Entrez/index.html Entrez] Biology search engine, e.g. for looking up protein and DNA sequences by name<br />[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed PubMed] Literature search<br />[http://www.ncbi.nlm.nih.gov/BLAST/ BLAST] Basic Local Alignment Search Tool, for DNA/protein alignment and comparison, primer verification, etc.<br /> </div> </div><div style="margin-left: 40px;">[http://scholar.google.com/ Google Scholar] Most general literature search tool. <br /><br /> </div><span style="font-style: italic;">Freeware:</span><br /><div style="margin-left: 40px;">[http://www.ipw.agrl.ethz.ch/%7Elhennig/wingene.html WinGene] Tool for analyzing nucleotide sequences. Best for reverse complements and primer checks.<br />[http://www.umass.edu/microbio/mfi/ MFI] For converting flow cytometer output files to ASCII. Simple free registration. <br />[http://www.openoffice.org/ OpenOffice.org] Open source office environment, fully compatible (well, almost) with MS Office, including Powerpoint.<br />[http://open-perl-ide.sourceforge.net/ Open Perl IDE] Open source Integrated Development environment for Perl. Easy to set up and use.<br />[http://www.activestate.com/Products/ActivePerl/?_x=1 ActivePerl] Easy installation for running Perl scripts in Windows; necessary for Open Perl IDE. <br /><br /> </div><span style="font-style: italic;">Perl scripts:<br /> </span><div style="margin-left: 40px;">[http://www.mit.edu/~mokelly/avo/deannotate_dna.pl deannotate_dna.pl] A useful script for annotating and editing DNA sequences. [http://www.mit.edu/~mokelly/avo/annotation%20documentation.txt This file] provides documentation and an example.<br />[http://www.mit.edu/~mokelly/avo/cytometry.zip cytometry.zip] Package of scripts and executables for quickly processing raw flow cytometer files into a table of histograms. Consult Michael on its use. <br /> </div><div style="margin-left: 40px;"> </div>

Revision as of 15:33, 10 April 2009



Reagents list
Restriction enzymes (-20C fridge)
Chores list
Books in the lab
Image Processing Tools


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>
Personal tools