GenNBPSeq: Generation of Never Born Protein Sequences
B.K.N. Muthugobal1, G. Ramesh2, S. Parthasarathy3* S. Suvaithenamudhan4 and K. Muthuvel Prasath3
1Department of Mathematics, Tamilavel Umamaheswaranar Karanthai Arts College, Karanthai, Thanjavur 613 002, Tamil Nadu, India
2Ramanujan Research Centre, Department of Mathematics, Government Arts College (Autonomous), Kumbakonam 612 001, Tamil Nadu, India
3Department of Bioinformatics, School of Life Sciences, Bharathidasan University, Tiruchirappalli 620 024, Tamil Nadu, India
4Department of Biotechnology and Bioinformatics, Bishop Heber College (Autonomous), Tiruchirappalli 620 017, Tamil Nadu, India
* For all correspondence bdupartha@gmail.com

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         The entire set of proteins can be considered as the union of three subsets namely the i) ‘Born’ (or) Natural proteins denoted by A, ii) ‘Never Born Proteins (NBPs)’ denoted as B and iii) ‘Cannot be Born’ (or) Impossible proteins denoted by C as given in Figure [Source: Muthugopal et al., BioSystems, 198 (2020) 104280]. The "GenNBPSeq" is an online web server [1] to generate a Never Born Protein (NBP) sequence and its corresponding DNA sequence, using the Partitioned Gray code representations of Universal Genetic Code combined with a novel Toeplitz matrix approach, as outlined in Muthugobal et. al. (2020)[2]. We generate the three sample NBP sequences NBP_SEQ_1, NBP_SEQ_2 and NBP_SEQ_3 using this "GenNBPSeq" online web server.

Choose Toeplitz Matrix Order

Click here for a brief Description of Generation of the three Sample NBP Sequences

Click here to get Sample Input and Output NBP_SEQ_1, NBP_SEQ_2 and NBP_SEQ_3

Click here to get Partitioned Toeplitz Matrix types PTM1, PTM2, PTM3 and PTM4

Click here for Universal Genetic Code

Click here for Supplementary data
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Figure. Diagrammatic representation of the entire
set of proteins, which includes three subsets of proteins.
(Source - Muthugobal et al., Biosystems, 198 (2020) 104280[2])

Please Cite
[1] B.K.N. Muthugobal, G. Ramesh, S. Parthasarathy, S. Suvaithenamudhan and K. Muthuvel Prasath (2022) GenNBPSeq: Online web server to generate Never Born Protein Sequences using Toeplitz Matrix Approach with Structure Analysis. Current Bioinformatics, 17(7), 565-577. http://dx.doi.org/10.2174/1574893617666220519110154.

[2] B.K.N. Muthugobal, G. Ramesh, S. Parthasarathy, S. Suvaithenamudhan and K. Muthuvel Prasath (2020) Gray code representation of the universal genetic code: Generation of never born protein sequences using Toeplitz matrix approach. Biosystems, 198, 104280. https://doi.org/10.1016/j.biosystems.2020.104280.

Patent
[1] B.K.N. Muthugobal, G. Ramesh, S. Parthasarathy, S. Suvaithenamudhan and K. Muthuvel Prasath (2019) "Generation of Never Born Protein Sequences using Toeplitz Matrix Approach" File number 201941004408. https://iprsearch.ipindia.gov.in/publicsearch.

Further Reference
He M, Petoukhov S and Ricci PE (2004) Genetic code, Hamming distance, and stochastic matrices. Bulletin of Mathematical Biology, 66, 965-973.

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