| Handout 2 |
get_points.m -
A simple Matlab function that extract 3D coordinates from a file pickCA.m - Matlab function to parse PDB files and extact CA coordinates make_contmap.m - Matlab script that plots the contact map of a protein structure |
| Handout 3 |
horner_eval.m -
A Matlab function that computes the value of a polynomial at a given point
using Horner's method poly_plot.m - Script that computes polynomial interpolations for x and y with respect to t, and plots x agains y spline_plot.m - Script that computes cubic spline interpolations for x and y with respect to t, and plots x agains y |
| Sequence Alignment Notes |
alignSequences.m -
Performs pairwise sequence alignment with fixed gap penalties getAlignmentScore.m - A Matlab function that computes the score of an aligment of two sequences pickSequence.m - Extract the sequence from a PDB file pos2sym.m - Converts integers between 1 and 20 to amino acid 1-letter codes pprintAlignment.m - "Pretty prints" a pairwise sequence alignment readScoreMatrix.m - Reads in the blosum 50 scoring matrix file sym2pos.m - Converts amino acid 1-letter codes to integers between 1 and 20 |