Impact of Parallel Computing on Bioinformatics Algorithms are well documented in this paper http://icacct.apiit.edu.in/download/all%20chapters/CHAPTER-44.pdf
Other useful links:http://icacct.apiit.edu.in/download/all%20chapters/
An excellent bioinformatics algorithms notes, and descriptive tutorial http://www.vaughaneveleigh.co.uk/wp-content/uploads/2012/02/Bioinformatics-Algorithms.pdf
Machine Learning Approaches to Bioinformatics http://www.asianscientist.com/books/wp-content/uploads/2013/06/7454_chap01.pdf
Other chapters of this book athttp://www.asianscientist.com/books/wp-content/uploads/2013/06/
I found a really good resource for Artificial Intelligence in Bioinformatics @ http://www.aisb.org.uk/publications/proceedings/aisb2000/AISB00_Bioinformatics.pdf
I found some good resources from AI articles, specifically from McGill University's COMP-644 (Pattern Recognition) course.
http://cgm.cs.mcgill.ca/~godfried/teaching/pr-web.html
Tree Edit Distance Problems: Algorithms and Applications to Bioinformatics @ http://repository.kulib.kyoto-u.ac.jp/dspace/bitstream/2433/139423/1/transinf.E93.D.208.pdf
Bioinformatics and Sequence Alignment tutorial by University of Illinois at Urbana-Champaign, Luthey-Schulten Group
http://www.ks.uiuc.edu/Training/Tutorials/science/bioinformatics-tutorial/bioinformatics.pdf
Machine Learning in Bioinformatics: Algorithms,Implementations & Applications thesis by Robert http://proteomics.bioengr.uic.edu/people/ezra/cv/thesis_uic.pdf
There are lots of books on bioinformatics algorithms, but I personally found this online book "Introduction to algorithms in bioinformatics" very easy to follow and...
Introduction to Bioinformatics Algorithms by Jones and Pevzner http://read.pudn.com/downloads160/ebook/722845/Intro%20to%20Bioinformatics%20Algorithms.pdf