Optimizing a program for analyzing RNA sequences

The program analyses and compares RNA sequences to correct tag assignments. The program was originally written in Perl, a natural choice when one wants to program string (= RNA sequence) operations. However, the performance can be very poor. In this project the cpu-intensive parts of the program were replaced by C, using SWIG. The resulting program runs about two orders of magnitude faster than the original one.

A detailed optimization report is available.