Answer:
Principles and Methods of Sequence Analysis
We aligned sequences by eye.
Troy CS, MacHugh DE, Bailey JF, Magee DA, Loftus RT, Cunningham P, Chamberlain AT, Sykes BC, Bradley DG. Genetic evidence for Near-Eastern origins of European cattle. Nature, 2001, vol. 410, p. 1091
This chapter is the longest in the book as it deals with both general principles and practical aspects of sequence and, to a lesser degree, structure analysis. Although these methods are not, in themselves, part of genomics, no reasonable genome analysis and annotation would be possible without understanding how these methods work and having some practical experience with their use. Inappropriate use of sequence analysis procedures may result in numerous errors in genome annotation (we have already touched upon this subject in the previous chapter and further discuss it in Chapter 5). We attempted to strike a balance between generalities and specifics, aiming to give the reader a clear perspective of the computational approaches used in comparative and functional genomics, rather than discuss any one of these approaches in great detail. In particular, we refrained from any extensive discussion of the statistical basis and algorithmic aspects of sequence analysis because these can be found in several recent books on computational biology and bioinformatics (see 4.8), and no less importantly, because we cannot claim advanced expertise in this area. We also tried not to duplicate the “click here”-type tutorials, which are available on many web sites. However, we deemed it important to point out some difficult and confusing issues in sequence analysis and warn the readers against the most common pitfalls. This discussion is largely based on our personal, practical experience in analysis of protein families. We hope that this discussion might clarify some aspects of sequence analysis that “you always wanted to know about but were afraid to ask”. Still, we felt that it would be impossible (and unnecessary) to discuss all methods of sequence and structure analysis in one, even long, chapter and concentrated on those techniques that are central to comparative genomics. We hope that after working through this chapter, interested readers will be encouraged to continue their education in methods of sequence analysis using more specialized texts, including those in the ‘Further Reading’ list (see 4.8).
