Abstract
In recent years, several experimental evidences suggest that amino acid repeats are closely linked to many disease conditions, as they have a significant role in evolution of disordered regions of the polypeptide segments. Even though many algorithms and databases were developed for such analysis, each algorithm has some caveats, like limitation on the number of amino acids within the repeat patterns and number of query protein sequences. To this end, in the present work, a new method called the internal sequence repeats across multiple protein sequences (ISRMPS) is proposed for the first time to identify identical repeats across multiple protein sequences. It also identifies distantly located repeat patterns in various protein sequences. Our method can be applied to study evolutionary relationships, epitope mapping, CRISPR-Cas sequencing methods, and other comparative analytical assessments of protein sequences.
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Acknowledgements
KS thanks the ICMR for funding the project ‘Do protein sequence repeats play a role in biological process and disease conditions’ (ISRM/12(34)/2020). KS, RS and DR thank the Center for Development of Advanced Computing (CDAC) for funding the project ‘An Indian Initiative on setting up a high-fidelity structural data archival/retrieval system for Life Sciences-(PDBi)’. RS thanks the Department of Science and Technology-Science and Engineering Research Board (DST-SERB), New Delhi, India, for providing research grant and postdoctoral fellowship (PDF/2019/000254). AM thanks Dr D S Kothari Postdoctoral Fellowship (BL/18-19/0320), funded by the University Grants Commission (UGC). All the authors thank the Department of Computational and Data Sciences, Indian Institute of Science, Bengaluru, India, for providing the necessary support.
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Prof. SK conceptualized the study. VKM and RS devised the methodology. AM, MS, RS and DR assessed the algorithm, methods. CNR and AM contributed to case studies. AM and RR wrote the manuscript. MS and CNR reviewed the manuscript.
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Maurya, V.K., Sanjeevi, M., Rahul, C.N. et al. Finding identical sequence repeats in multiple protein sequences: An algorithm. J Biosci 49, 41 (2024). https://doi.org/10.1007/s12038-023-00410-x
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DOI: https://doi.org/10.1007/s12038-023-00410-x