A new trainable, high-speed and biologically relevant alignment algorithms of high-throughput sequencing reads to coding DNA http://nar.oxfordjournals.org/content/early/2014/05/26/nar.gku473.full
The FindMotif.pl program uses position-specific scoring matrices to search for sequences similar to a consensus sequence. Find more at http://www.people.vcu.edu/~elhaij/IntroBioinf/Notes/PSSM-Perl.html
A lecture notes series by Can Alkan and Shatlyk Ashyralyev on Introduction to Bioinformatics Algorithms: A Computational Molecular Biology Approaches can be found at http://www.cs.bilkent.edu.tr/~calkan/teaching/cs481/