Abstract:
Proteins have been classified into families based on metrics of similarity such as sequence or structural similarity. However, there are significant differences in functi...Show MoreMetadata
Abstract:
Proteins have been classified into families based on metrics of similarity such as sequence or structural similarity. However, there are significant differences in function even within families. For example, only a subset of the family of matrix metalloproteinases is capable of cleaving collagen. Typically, a scientist scans multiple sequence alignment by eye to find amino acids that might be responsible for differences in functionality. This is based on a set of parametric rules using log-odds scores from amino acid substitution matrices and a multiple sequence alignment. ConsDiff is a Web server-based implementation of this approach that uses ClustalW to generate a multiple sequence alignment and then highlights conserved differences between two sets of sequences. ConsDiff offers flexibility in thresholds of detection and the choice of several PAM/BLOSUM matrices, or a user specified matrix or alignment. This allows the automated discovery of candidate residues that may be responsible for critical differences in function, which may then be experimentally verified.
Published in: 14th International Workshop on Database and Expert Systems Applications, 2003. Proceedings.
Date of Conference: 01-05 September 2003
Date Added to IEEE Xplore: 15 September 2003
Print ISBN:0-7695-1993-8
Print ISSN: 1529-4188