CUSP: an algorithm to distinguish structurally conserved and unconserved regions in protein domain alignments and its application in the study of large length variations |
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| Authors: | Sankaran Sandhya Barah Pankaj Madabosse Kande Govind Bernard Offmann Narayanaswamy Srinivasan Ramanathan Sowdhamini |
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| Affiliation: | 1.National Centre for Biological Sciences (TIFR),Bangalore,India;2.Mathematical modeling and Computational Biology group,Centre for Cellular and Molecular Biology,Hyderabad,India;3.Laboratoire de Biochimie et Génétique Moléculaire,Université de La Réunion,La Réunion,France;4.Molecular Biophysics Unit,Indian Institute of Science,Bangalore,India |
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| Abstract: | Background Distantly related proteins adopt and retain similar structural scaffolds despite length variations that could be as much as
two-fold in some protein superfamilies. In this paper, we describe an analysis of indel regions that accommodate length variations
amongst related proteins. We have developed an algorithm CUSP, to examine multi-membered PASS2 superfamily alignments to identify
indel regions in an automated manner. Further, we have used the method to characterize the length, structural type and biochemical
features of indels in related protein domains. |
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