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Introduction to Bioinformatics. T.K Attwood and DJ Parry-Smith. Addison Wesley Longman, Harlow; 1999; ISBN 0 582 327881

Bioinformatics: Genes, Proteins & Computers .Orengo C.A.. et al.. Advanced Text,  BIOS Scientific Publishers, 2003

Madera M. and Gough J. 2002. A comparison of profile hidden Markov model procedures for remote homology detection. Nucleic Acids Research, 30 (19) 4321-4328

Thompson J.D., Plewniak F., Poch O. 1999. A comprehensive comparison of multiple sequence alignment programs. Nucleic Acids Research, 27 (13) 2682-2690
 

Recommended courses

Online course:  InterPro: Quick tour

Online course: InterPro: Functional and structural analysis of protein sequences

The EBI offers hands-on courses coveraing a range of subjects, including training on InterPro.  An up-to-date list of training courses is available here.