We identify and describe a set of tools readily available for integral membrane 
protein prediction. These tools address two problems: finding potential 
transmembrane proteins in a pool of new sequences, and identifying their 
transmembrane regions. All methods involve comparing the query protein against 
one or more target models. In the simplest of these, the target "model" is 
another protein sequence, while the more elaborate methods group together the 
entire set of t ansmembrane helical or transmembrane beta-barrel proteins. In 
general, prediction accuracy either in identifying new integral membrane 
proteins or transmembrane regions of known integral membrane proteins depends 
strongly on how closely the query fits the model. Because of this, the best 
approach is an opportunistic one: submit the protein of interest to all methods 
and choose the results with the highest confidence scores.