Bio-recipes

Bio-recipes are a collection of Darwin example programs. They show how to solve standard problems in Bioinformatics. Each bio-recipe consists of an introduction, explanations, graphs, figures, and most importantly, Darwin commands (the input commands and the output that they produce) that solve the given problem.

Each recipe contains Darwin statements shown in green, Darwin output in red and comments in black. The comments include a short description about the problem that is solved in the recipe, and about the algorithm that is used to produce the solution.

The intended method of usage for the Bio-recipes is that after reading the explanatory text, the Darwin statment can be copied (cut and paste) to a Darwin prompt. The Darwin output can then be compared to what is given as output in the recipe. If you have to solve a slightly different task from what is shown in the recipe, you can always copy the Darwin statements into a text editor. There you can modify the statements such that your specific problem can be solved.

Bio-recipes tied to biological questions
Total Number of Pairs of Amino Acids in the SwissProt Database
Unbiased selection of sample alignments
Finding Orthologous sequences and building a phylogenetic tree
Significance assessment of an alignment
Multiple repetitions of a short motif
Sequence Alignments with Special Characteristics
Recognizing Proteins by Weight of their Digested Parts
The most significant Codon Bias in Yeast
Virus Classification using k-nucleotide Frequencies
Determination of Haplotypes from Genotype information
Computing Confidence Levels for Quartets
Mathematical / algorithmical topics
Chi-square Test for a Contingency Table of Counts
Linear Regressions: 5 Methods to Compute A^t * A
String Alignment using Dynamic Programming
Linear Classification or Discrimination
The tRNA Pairing Index
How to Compute Mutation and Dayhoff Matrices
Introduction to Codon Substitution Matrices
Idealized Mutational Clocks
Programming in Darwin
Basic introduction to programming in Darwin
Counters: an example of a simple Class
Linear algebra in Darwin
Search your Name in the SwissProt Database
A Class for Discrete Bayesian Networks in Darwin
Phylogenetic tree of the "Nigerian Prince" email scam
Random Distance Trees, analysis of properties
Back Translation (protein to DNA) in an optimal way
Significance of Alignment Scores
Bio-recipes