Software Listing of Author : "Brad Ridder"

MOTIFINFO = GIBBSMOTIFSAMPLER(SEQARRAY,MOTIFVECTOR,ALPHABET,OPTIONS) Searches for the motifs in a set of sequences via Gibbs sampling. seqArray is a cell vector of sequence strings. motifVector is a vector of uniformly-spaced motif widths you wish to optimize. The program iterates over these widths, and returns the one that is the "best", according the technique described in Lawrence et al, Science, Vol. 262, No. 5131 pp. 208-214, 1993. alphabet is a string that denotes the alphabet you want to use. Use 'DNA' to use 'ATCG', or 'Protein' to use 'ARNDCEQGHILKMFPSTWYV'. You can enter one in of your choice as well. Options is the options structure, which has some nifty features. The fields are: nTrials: The number of trials to perform for each motif alignment. The more the better, but the longer it takes. pcMode:...

  • Platform: Matlab, Scripts

From undergraduate chemistry, we know how to test whether a reaction is 0th, 1st, or 2nd order by plotting different transformations of the data, and inspecting which plot fits the best. This program does the same thing. It transforms the data using different values of the order, attempting to maximize the Pearson r-squared value. Its much faster than making and inspecting a multitude of different plots. The picture above is essentially an example. I used the Wikipedia article for the n-th order transformation equation. (http://en.wikipedia.org/wiki/Rate_equation#Summary_for_reaction_orders_0.2C_1.2C_2_and_n)

  • Platform: Matlab, Scripts

Handy little function, for those of you in lab classes where they are sticklers for error. (or for those of you that are actual scientists even...!). Propagation of uncertainty is a really slick formula, but its a massive pain to do by hand. this function does it for you! To do it, just enter in the symbolic function, a row vector of the variables, a row vector for the estimated values of those variables, and lastly a row vector of the uncertainty associated with those variables. help PropError has an example in it. Enjoy! outputs both actual error, and the percent error. The program follows the equation shown in the screenshot. (courtesy of Wikipedia). Requires Symbolic Math Toolbox.

  • Platform: Matlab, Scripts

For a symbolic input function f, returns the symbolic Hessian matrix. A real time saver imho I don't know how useful anyone will find this, but eh, my professor made us do it on the test, so I figure this will save at least someone the headache of having to find the Hessian by hand (provided they are allowed to use computers). Requires Symbolic Math Toolbox.

  • Platform: Matlab, Scripts
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