Practical Database Searching

trends guide to bioinformatics 0167-7799/98/$ – see front matter © 1998 Elsevier Science. All rights reserved. More sequences have been putatively characterized by database searches than by any other single technology. For good reason: programs like BLAST are fast and reliable. However, sequence comparison procedures should be treated as experiments analogous to standard laboratory procedures.Their use deserves the same care both in the design of the experiment and in the interpretation of results. The database search experiment Design of a BLAST database search requires consideration of what information is to be gained about the query sequence of interest. The main constraint is that database searching can only reveal similarity. However, from this similarity, homology (i.e. evolutionary relationship) can be inferred and, from that, one might be able to infer function. Although the former inference is now reliable Steven E. Brenner Dept of Structural Biology, Stanford University, Stanford, CA 94305-5400, USA. [email protected] Practical database searching