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Lesk: Introduction to Bioinformatics: 3e

Chapter 05

Altschul, S.F. and Koonin, E.V. (1998). Iterated profile searches with PSI-BLAST-a tool for discovery in protein databases. Trends in Biochemical Sciences, 23, 445-447. Description of one of the most important tools for database searching for sequence similarity. [DOI: 10.1016/S0968-0004(98)01298-5]

Altschul, S.F., Boguski, M.S., Gish, W. and Wootton, J.C. (1994). Issues in searching molecular sequence databases. Nature Genetics, 6, 119-129. General background to challenges in designing information-retrieval methods and interpreting the results. [PubMed: 8162065] [DOI: 10.1038/ng0294-119]

Eddy, S. (1996). Hidden Markov models. Current Opinion in Structural Biology, 6, 361-365. Readable introduction to an important mathematical technique providing powerful tools for detection of distantly related sequences, and protein fold recognition. [PubMed: 8804822] [DOI: 10.1016/S0959-440X(96)80056-X]

Efron, B. and Gong, G. (1983). A leisurely look at the bootstrap, the jackknife, and cross-validation. The American Statistician, 37, 36-48. Classic paper on statistical methods for calibrating pattern recognition procedures. [DOI: 10.2307/2685844]

Penny, D., Hendy, M.D., Zimmer, E.A. and Hamby, R.K. (1990). Trees from sequences: panacea or Pandora's box? Australian Systematic Botany, 3, 21-38. Cautionary notes about determination of phylogenetic trees. [DOI: 10.1071/SB9900021]

Smith, T.F. (1999). The art of matchmaking: sequence alignment methods and their structural implications. Structure, 7, R7-R12. Explanation of different sequence alignment methods, and what can confidently be concluded from them about similarity of structure. Gives due emphasis to structure-based alignment as a 'gold standard'. [PubMed: 10368278] [DOI: 10.1016/S0969-2126(99)80003-3]