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Title

Prediction and analysis of paralogous proteins in Trichomonas vaginalis genome 

Authors

Satendra Singh1, Gurmit Singh2, Atul Kumar Singh3, Budhayash Gautam1, Rohit Farmer1, Sharad S Lodhi4, Gulshan Wadhwa4* 

Affiliation

1Department of Computational Biology & Bioinformatics, JSBB, SHIATS, Allahabad-211007, India; 2Department of Computer Science and Information Technology, CET, SHIATS, Allahabad-211007, India; 3Department of Biotechnology, Madhav Institute of Technology and Science, Gwalior 474005, India; 4Department of Biotechnology, Ministry of Science &Technology, New Delhi- 110003, India 

Email

gulshan@dbt.nic.in; *Corresponding author

Phone

+91-9811301820

 

Fax

+91-11-24362884

 

Article Type

Hypothesis

 

Date

Received February 07, 2010; Accepted February 21, 2010; Published March 02, 2011

 

Abstract

Trichomonas vaginalis causes trichomoniasis, second most sexually transmitted disease. The genome sequence draft of T. vaginalis was published by The Institute of Genomic Research reveals an abnormally large genome size of 160 Mb. It was speculated that a significant portion of the proteome contains paralogous proteins. The present study was aimed at identification and analysis of the paralogous proteins. The all against all search approach is used to identify the paralogous proteins. The dataset of proteins was retrieved from TIGR and TrichDB FTP server. The BLAST-P program performed all against all database searches against the protein database of Trichomonas vaginalis available at NCBI genome database. In the present study about 50,000 proteins were searched where 2,700 proteins were found to be paralogous under the rigid selection criteria. The Pfam database search has identified significant number of paralogous proteins which were further categorized among different 1496 paralogous protein in pfam families, 1027 paralogous protein contains domain, 60 proteins were having different repeats and 1092 paralogous protein sequences of clans. Such identification and functional annotation of paralogous proteins will also help in removing paralogous proteins from possible drug targets in future. Presence of huge number of paralogous proteins across wide range of gene families and domains may be one of the possible mechanisms involved in the T. vaginalis genome expansion and evolution.  

Keywords

T. vaginalis, pseudogenes, Paralogous proteins

 

Citation

Singh et al. Bioinformation 6(1): 31-34 (2011)

Edited by

AU Khan

 

ISSN

0973-2063

 

Publisher

Biomedical Informatics

 

License

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.