This page is meant to collect pointers to programs which compute useful things about DNA, e.g. melting temperatures, secondary structure, molecular dynamics, etc. I haven't actually used many of them yet. Other good resources include CMS MBR.
These are my own routines. They are extremely rough, commonly inaccurate and buggy, and come only with the guarantee that they'll goof up at least once. However, if you like dinking around with MATLAB, they may come in handy. There are routines for evaluating sequences in several ways -- e.g. delta-G, dot plots, unintended Watson-Crick complementary regions -- and for optimizing a sequence that both satisfies hard criteria (base pairing requirements, specific base assignments) and minimizes soft costs (number of unintended domains, etc.). All the routines are written in MATLAB, and are thus available for you to modify, examine, and use in your own code.
THIS IS AN ALPHA RELEASE. THERE ARE SURELY BUGS. USE AT YOUR OWN RISK. THIS CODE WILL BE CHANGING DRAMATICALLY AS I NEED TO USE IT FOR NEW PURPOSES IN MY RESEARCH.
The file is a gzipped tar archive. Upon gunzipping it, and untarring it, it will create a directory called DNAdesign-0.?? containing the MATLAB files. You will want to compile some of the functions... see "notes-examples" for a very brief and informal tutorial. I can provide the package in other formats if requested.
NAMOT is a 3D modelling system designed for visuallizing unusual DNA structures. They have a nifty example of Ned Seeman's cube, and I've been able to come up with "reasonable-looking" models of double-crossover molecules.
Predicting DNA and RNA secondary structure:
mfold for DNA.Zuker has some of the best-known and most publicly available RNA and DNA folding algorithms, which find loop-type secondary structure.
Poland: compute thermal denaturation profile for RNA or DNA. Tm: melting temperature for oligonucleotides. Extinction coefficients. Oligo vital statistics. ALIGN: align two sequences. Also LALIGN, LFASTA. CLUSTALW: align multiple sequences. STS Pipeline: Design primers for PCR. Predicts secondary structure of single linear or circular DNA strand. ALSO HAS EXCELLENT LINKS.
PrimerDesign and related resources. NIH Molecular Modeling Overview. MC-SYM structure prediction developed at U Montreal. Runs on UNIX. Amber molecular dynamics package developed at UCSF. Runs on UNIX, VMS, DOS. Resource page. Pittsburg Supercomputing Center nucleic acid & protein analysis tools. SCULPT: commercial SGI and Mac package for interactive design of molecules. Biosym: commercial molecular simulation software. MidasPlus molecular modelling system developed at UCSF. MacroModel molecular modelling system developed at Columbia. Runs on SGI an RS/6000.
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