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PPS: A computing engine to find Palindromes in all Protein sequences



Zameer Ahmed, Manickam Gurusaran, Prasanth Narayana, Kala Sekar Dinesh Kumar, Jayapal Mohanapriya, Marthandan Kirti Vaishnavi & Kanagaraj Sekar*



Supercomputer Education and Research Centre, Indian Institute of Science, Bangalore 560 012, India


Email; *Corresponding authors


Article Type




Received January 05, 2014; Revised January 23, 2014; Accepted January 24, 2014; Published January 29, 2014



The primary structure of a protein molecule comprises a linear chain of amino acid residues. Certain parts of this linear chain are unique in nature and function. They can be classified under different categories and their roles studied in detail. Two such unique categories are the palindromic sequences and the Single Amino Acid Repeats (SAARs), which plays a major role in the structure, function and evolution of the protein molecule. In spite of their presence in various protein sequences, palindromes have not yet been investigated in detail. Thus, to enable a comprehensive understanding of these sequences, a computing engine, PPS, has been developed. The users can search the occurrences of palindromes and SAARs in all the protein sequences available in various databases and can view the three-dimensional structures (in case it is available in the known three-dimensional protein structures deposited to the Protein Data Bank) using the graphics plug-in Jmol. The proposed server is the first of its kind and can be freely accessed through the World Wide Web.






Single Amino Acid Repeats, computing engine, three-dimensional crystal structures, Palindromes.



Ahmed  et al. Bioinformation 10(1): 048-051 (2014)


Edited by

P Kangueane






Biomedical Informatics



This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.