We apologize for a recent technical issue with our email system, which temporarily affected account activations. Accounts have now been activated. Authors may proceed with paper submissions. PhDFocusTM
CFP last date
20 December 2024
Call for Paper
January Edition
IJCA solicits high quality original research papers for the upcoming January edition of the journal. The last date of research paper submission is 20 December 2024

Submit your paper
Know more
The week's pick
Responsive image
Improved Shuffled Frog Leaping Algorithm with Self-Adaptive Shuffling for Fuzzy Logic PD+G Controller Optimization in Robotic Manipulators

Duc Hoang Nguyen
Random Articles
Reseach Article

Comparative Functional Genomics Studies for Understanding the Hypothetical Proteins in Mycobacterium tuberculosis KZN 1435

by Swapnil Sanmukh, Sumita Goswami, Sandhya Swaminathan, Waman Paunikar
journal cover thumbnail

International Journal of Computer Applications
Foundation of Computer Science (FCS), NY, USA
Volume 60 - Number 1
Year of Publication: 2012
Authors: Swapnil Sanmukh, Sumita Goswami, Sandhya Swaminathan, Waman Paunikar
10.5120/9653-3943

Swapnil Sanmukh, Sumita Goswami, Sandhya Swaminathan, Waman Paunikar . Comparative Functional Genomics Studies for Understanding the Hypothetical Proteins in Mycobacterium tuberculosis KZN 1435. International Journal of Computer Applications. 60, 1 ( December 2012), 1-3. DOI=10.5120/9653-3943

@article{ 10.5120/9653-3943,
author = { Swapnil Sanmukh, Sumita Goswami, Sandhya Swaminathan, Waman Paunikar },
title = { Comparative Functional Genomics Studies for Understanding the Hypothetical Proteins in Mycobacterium tuberculosis KZN 1435 },
journal = { International Journal of Computer Applications },
issue_date = { December 2012 },
volume = { 60 },
number = { 1 },
month = { December },
year = { 2012 },
issn = { 0975-8887 },
pages = { 1-3 },
numpages = {9},
url = { https://ijcaonline.org/archives/volume60/number1/9653-3943/ },
doi = { 10.5120/9653-3943 },
publisher = {Foundation of Computer Science (FCS), NY, USA},
address = {New York, USA}
}
%0 Journal Article
%1 2024-02-06T21:05:27.403444+05:30
%A Swapnil Sanmukh
%A Sumita Goswami
%A Sandhya Swaminathan
%A Waman Paunikar
%T Comparative Functional Genomics Studies for Understanding the Hypothetical Proteins in Mycobacterium tuberculosis KZN 1435
%J International Journal of Computer Applications
%@ 0975-8887
%V 60
%N 1
%P 1-3
%D 2012
%I Foundation of Computer Science (FCS), NY, USA
Abstract

The prediction for the unknown proteins from Mycobacterium tuberculosis KZN 1435 were carried out for characterization of the proteins in their respective families. In Mycobacterium tuberculosis KZN 1435 out of 1560 genes for hypothetical proteins, functions were predicted for 1221 hypothetical protein whereas, structures for 803 unknown proteins were revealed. The Bioinformatics web tools like CDD-BLAST, INTERPROSCAN, PFAM and COGs were used for the prediction of functions in the proteins by searching protein databases for the presence of conserved domains; whereas, tertiary structures were constructed using PS2 Server-Protein Structure Prediction server. This study was helpful in understanding functional characteristics of hypothetical proteins in Mycobacterium tuberculosis KZN 1435 as well as their role in the life cycle of the bacterium.

References
  1. Murray M, Pillay M, Borowsky ML. , Young SK, Zeng Q, Koehrsen M, Alvarado L, Berlin AM, Borenstein D, Chen Z, Engels R, Freedman E , Gellesch M, Goldberg J, Griggs A, Gujja S, Heiman DI. , Hepburn,T. A. , Howarth,C. , Jen,D. , Larson,L. , Lewis,B. , Mehta,T. , Park,D. , Pearson M, Roberts A, Saif S, Shea TD, Shenoy N, Sisk P, Stolte C, Sykes SN. , Walk T, White J, Yandava C. , Haas B, Nusbaum C, Galagan J and Birren B. The Genome Sequence of Mycobacterium tuberculosis strain KZN 1435 (Unpubli
  2. Neel RG, Anthony MA, Willem S, Robert P, Thiloshini G, Umesh L, Kimberly Z, Jason A, Gerald F. Extensively drug-resistant tuberculosis as a cause of death in patients co-infected with tuberculosis and HIV in a rural area of South Africa. The Lancet, 368, 1575 - 1580, (2006).
  3. Edward E, Gary LG. , Osnat H, John M, John O, Roberto JP, Linda B, Delwood R. , Andrew J H. Biological function made crystal clear- annotation of hypothetical proteins via structural genomics. Current Opinion in Biotechnology 11, 25-30, (2000).
  4. Swapnil GS, Waman NP, Tarun, KG. Study of Hypothetical Proteins in Salmonella Phages and Predicting their Structural and Functional Relationship CiiT International Journal of Biometrics and Bioinformatics. DOI: BB022011001, (2011).
  5. Swapnil GS, Dilip, B. M. , Waman NP, Tarun, KG. Computational characterizations for structure and function of unclassified proteins in Ictalurus punctatus. CiiT International Journal of Artificial Intelligent Systems and Machine Learning DOI: AIML052011001, (2011).
  6. Swapnil GS, Waman NP. Study of hypothetical proteins in Shigella phages. CiiT International Journal of fuzzy Systems DOI: FS062011002, (2011).
  7. Swapnil GS, Waman NP, Dilip, BM. , Tarun, KG. Functionality search in hypothetical proteins of Halobacterium salinarum. CiiT International Journal of fuzzy Systems DOI: FS062011001, (2011).
  8. Swapnil GS, Waman NP, Dilip BM. , Tarun, KG. Insilico function prediction for hypothetical proteins in Vibrio parahaemolyticus Chromosome II. CiiT International Journal of Data Mining and Knowledge Engineering. DOI: DMKE052011003, (2011).
  9. Swapnil GS, Waman NP, Tarun, KG & Tapan, C. Structural & functional prediction of hypothetical Proteins In bacteriophages against halophilic bacteria - an in silico approach. Int J Pharm. Bio. Sci. Vol 2 (2), B61-B70, (2011)
  10. Swapnil GS, Waman NP, Tarun, KG. & Tapan, C. Structure and Function Predictions of Hypothetical Proteins in Vibrio Phages. International Journal of Biometrics and Bioinformatics. 4, 161-175, (2010).
  11. Swapnil GS, Waman NP, Tarun, KG. Computational approach for structure and functionality search for hypothetical proteins in Mycobacterium leprae CiiT International Journal of Data Mining and Knowledge Engineering DOI: DMKE032011014, (2011).
  12. Zafer, A. , Yucel, A. , Mark, B. Protein secondary structure prediction for a single-sequence using hidden semi-Markov models, BMC Bioinformatics ,7, 178, (2006).
  13. Altschul SF. , Madden TL. , Schaffer AA. , Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25 (17), 3389-402, (1997).
  14. Chih-Chieh C, Jenn-Kang H, Jinn-Moon Y (PS)2: protein structure prediction server Nucl. Acids Res. 34, W152-W157, (2006).
  15. Alejandro AS, Aravind L, Thomas LM, Sergei S, John LS, Yuri IW, Eugene VK, Stephen F A. Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements. Nucleic Acids Res. 29(14), 2994-3005, (2001).
  16. Aron MB, John BA, Myra KD, Carol DS, Noreen RG, Marc G, Luning H, Siqian H, David IH, John DJ, Zhaoxi K, Dmitri K, Christopher JL, Cynthia AL, Chunlei L, Fu L, Shennan L, Gabriele HM, Mikhail M, James SS. , Narmada T, Roxanne AY. , Jodie JY, Dachuan Z, Stephen HB. CDD: a conserved domain database for interactive domain family analysis. Nucleic Acids Research, Vol. 35, D237–D240, (2006).
  17. Zdobnov, E. M. , Rolf, A. Interproscan- an integration platform for the signatures recognition methods in InterPro. Bioinformatics 17,847-848, (2001).
  18. Alex B, Lachlan C. , Richard D, Robert DF. , Volker H, Sam GJ, Ajay K, Mhairi M, Simon M, Erik LLS. , David JS. , Corin Y, Sean RE. The Pfam families' database. Nucleic Acids Research, Vol. 32, D138-D141, (2004).
  19. Roman LT, Michael YG, Darren AN, Eugene VK. The COG database: a tool for genome –scale analysis of protein functions and evolution. Nucleic Acid Research. 28, 33-36, (2000).
  20. Cédric N, Desmond GH, Jaap H. T-coffee: a novel method for fast and accurate multiple sequence alignment. J. Mol. Biol. 302, 205-217, (2000).
  21. Canchaya C, Proux C, Fournous G, Bruttin A, Brussow H. Prophage genomics. Microbiol Mol Biol Rev 67: 238–276, 2003.
  22. Casjens S. Prophages and bacterial genomics: what have we learned so far? Mol Microbiol 49: 277–300, (2003).
Index Terms

Computer Science
Information Sciences

Keywords

Unknown proteins Bioinformatics web tools protein databases tertiary structures functional characteristics

Powered by PhDFocusTM