Biosequence Algorithms (Spring 2005) Links

General Molecular Biology and Bioinformatics

• The Double Helix (the chemical structure of DNA in a nutshell)
• Introduction to Molecular Biology; notes (Postscript) of a lecture by Beth Simpson, written down by D. Fenger and edited by S. Griffiths.
• Bioinformatiikan sanasto (English-Finnish glossary of bioinformatics; CSC; Heikkinen, Korpi, Mattila, Porali, and Vihinen)
• European Bioinformatics Institute
• IEEE/ACM Transactions on Computational Biology and Bioinformatics (started in 2004)

Suffix Trees and Related Stuff

• Classified links related to Suffix Trees
  • including a good-looking tutorial by L. Allison
• "Efficient implementation of suffix trees", an article by A. Andersson and S. Nilsson, appeared in Software - Practice and Experience, 25(2):129-141, 1995.
• Juha Kärkkäinen and Peter Sanders. Simple linear work suffix array construction. In Proc. 30th International Colloquium on Automata, Languages and Programming (ICALP '03). LNCS 2719, Springer, 2003, pp. 943-955. Available on Juha Kärkkäinen's home page
• Juha Kärkkäinen and S. Srinivasa Rao. Full-Text Indexes in External Memory. Chapter 7 in U. Meyer, P. Sanders, J. Sibeyn (eds.), Algorithms for Memory Hierarchies (Advanced Lectures). LNCS 2625, Springer 2003, pp. 149-170. Available on Juha Kärkkäinen's home page

Software

• Homepage of strmat, "collection of C programs tied together with a simple menu system that implement a variety of string matching and pattern discovery algorithms", by D. Gusfield et al.
• BLAST
  • Illustration of the BLAST search algorithm
• FASTA
  • WWW search page at the U. of Virginia
  • The FASTA package of sequence comparison programs