Chapter category: Bioinformatics
Prediction of Protein Function Two Basic Concepts and One Practical Recipe
Chapter authors:
Frank Eisenhaber
The analysis of uncharacterized biomolecular sequences obtained as a result of genetic screens, expression profile studies, etc. is a standard task in a life science research environment. The understanding of protein function is typically the main difficulty. This chapter intends to give practical advise to students and researchers that have only introductory knowledge in the field of protein sequence analysis. The theoretical approaches applicable range from (1) textual analyses, interpretation in terms of patterns of physical properties of amino acid side chains and (2) the extrapolation of empirically established relationships between local sequence motifs with known structural and functional properties to the collection of sequence segment families with sequence distance metrics and protein function derivation with annotation transfer (concept of homologous families). Here, the impact of different techniques for the biological interpretation of targets is discussed from the practitioner’s point of view and illustrated with examples from recent research reports. Although sequence similarity searching techniques are the most powerful instruments for the analysis of high-complexity regions, other techniques can supply important additional evaluations including the assessment of applicability of the sequence homology concept for the given target segment.
