NDLI: ConsDiff: identification of conserved differences between sets of amino acid sequences

Content Provider	IEEE Xplore Digital Library
Author	Mehta, S. Dinakarpandian, D.
Copyright Year	2003
Description	Author affiliation: Sch. of Comput. & Eng., Missouri-Kansas Univ., Kansas, MO, USA (Mehta, S.; Dinakarpandian, D.)
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.
Starting Page	21
Ending Page	24
File Size	222613
Page Count	4
File Format	PDF
ISBN	0769519938
ISSN	15294188
DOI	10.1109/DEXA.2003.1231992
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2003-09-01
Publisher Place	Czech Republic
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Amino acids Cities and towns Matrices Computer science Electronic mail Protein engineering Conferences Databases Expert systems
Content Type	Text
Resource Type	Article

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