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