RSAT - Wish list

This page contains a list of ideas to be implemented when I will find some time to do it    :-(

Date wish emitted Program Description
2005/04/09 compare-features
  • A program to compare two lists of features. Useful for evaluating pattern matching results.
  • The comparisons will be performed either at the nucleotide level or at the site level (with a threshold on the mathcing nucleotides per pair of sites).
  • This program will compare a query and a reference set of positions and return intersection, differences, calculate TP, FP, FN, TN, and derived statistics.
2005/04/09 convert-markov-model
  • Read and write Markov models in different formats (oligo-analysis, meme, Motifsampler).
2005/04/09 convert-matrix
  • Export all matrices when the input file contains several of them (e.g. consensus, meme, gibbs).
  • Calculate the significance sig=-log10(P-value) of each letter at each position. The P-value would be calculated with a binomial model.
  • Improve the criterion to include a letter in the consensus (use significance rather than weight ?).
2005 dyad-analysis
  • The statistics for counts on 2 strands is still in the old mode (single pattern probability, double sequence length). I should adapt it in the same way as oligo-analysis.