First of all:
Application's Help files and FAQ's
Books:
Essential Bioinformatics. Jin Xiong. Cambridge University Press, 2006
Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins, Third Edition. Eds. A.D. Baxevanis and B.F.F. Oulette - click here
Introduction to Bioinformatics. A Theoretical and Practical Approach. Edited by Stephen A. Krawetz and David D. Womble. Humana Press, Totowa, New Jersey, 2003
Grzegorz Bartoszewski's course main page