Integrated web service for improving alignment quality based on segments comparison
Defining blocks forming the global protein structure on the basis of local structural regularity is a very fruitful idea, extensively used in description, and prediction of structure from only sequence information. Over many years the secondary structure elements were used as available building blocks with great success. Specially prepared sets of possible structural motifs can be used to describe similarity between very distant, non-homologous proteins. The reason for utilizing the structural information in the description of proteins is straightforward. Structural comparison is able to detect approximately twice as many distant relationships as sequence comparison at the same error rate.
library of protein motifs profile-profile sequence similarity (blast ffas) fragments library (fraglib) predicted local structure segments (plsss) segment alignment (sea) network matching problem