INSILICO CHARACTERIZATION OF UNCHARACTERIZED PROTEINS IN MUS MUSCULUS (STRAIN C57BL/6)

PROJECT REPORT
submitted in partial fulfillment of the requirements for the award of the degree of BACHELOR OF TECHNOLOGY in BIOINFORMATICS by

Aishwarya Varsha

(11207003)

Bharat Phani Vaikuntam (11207018) Bhupendra Khandelwal (11207019)

under the guidance of Mr. P.P. Karthikeyan (Assistant Professor, Department of Bioinformatics)

DEPARTMENT OF BIOINFORMATICS SCHOOL OF BIOENGINEERING FACULTY OF ENGINEERING AND TECHNOLOGY SRM UNIVERSITY KATTANKULATHUR 603 203

May 2011

CERTIFICATE

Certified that this dissertation entitled Insilico characterization of uncharacterized proteins in MUS MUSCULUS (strain C57BL/6) is a bonafide work done by Aishwarya Varsha (11207003), Bharat Phani Vaikuntam (11207018) and Bhupendra Khandelwal (11207019) of IV YEAR B.Tech Bioinformatics, SRM University, who carried out the project under my guidance and supervision. It is further certified that to the best of my knowledge the work reported here in, does not form a part of any thesis or dissertation on the basis of which degree was awarded on an earlier occasion and this work should not be published without prior written permission.

INTERNAL GUIDE

HEAD OF THE DEPARTMENT

DATE:

INTERNAL EXAMINAR

EXTERNAL EXAMINAR

ACKNOWLEDGEMENT

We would like to express our earnest appreciation to everyone who has taken part in the successful completion of this work The sincere efforts put with great interest were from Prof. Dr. Waheeta Hopper, our Head of the Department of Bioinformatics by providing valuable suggestions and clarifications which is thankfully appreciated. We wish to express our sincere gratitude to Mr. P.P. Karthikeyan, project guide for his guidance and supervision in this project. His concern has been the driving force for us all through this project. We are thankful for his constant advice and encouragement. Our special thanks to project head Dr. N. Rathankar for his support advice to improve the project. We intently thank all our department staff members for their valuable guidance provided in completing the work successfully.

Aishwarya Varsha

(11207003)

Bharat Phani Vaikuntam (11207018) Bhupendra Khandelwal (11207019)

LIST OF FIGURES

Figure 1. Figure 2.

MUS MUSCULUS C57BL6 Exploring the MUS MUSCULUS genome using Ensembl site tool

Figure 3. M.musculus chromosome database via EBI-FTP Figure 4. Trademark Geneious Pro Figure 5. Filtering using Geneious Pro Figure 6. Checking for the structures at Protein Model Portal(PMP). Figure 7. Submitting the sequences to ModWeb server Figure 8. Sequence submission to ClustalW2 Figure 9. Function analysis using Blast2Go

Figure 10. 3D Structures obtained from ModWeb Server on the email-id provided Figure 11. 3D Structure obtained from ModWeb Figure 12. Part of Phylogenetic tree obtained from ClustalW2 results Figure 13. Blast results obtained from Blast2Go tool Figure 14. InterproScan results obtained from Blast2Go tool Figure 15. PPP obtained from Blast2Go tool Figure 16. Biosynthesis of Ansamysins pathway obtained from Blast2Go tool Figure 17. Carbon Fixation in Photosynthetic Organisms pathway obtained from Blast2Go tool Figure 18. Glycerophospholipid Metabolism pathway obtained from Blast2Go tool

Figure 19. Pyrimidine Metabolism pathway obtained from Blast2Go tool Figure 20. Purine Metabolism pathway obtained from Blast2Go tool Figure 21. GO results obtained from Blast2Go tool Figure 22. Structure prediction statistics of sex chromosomes of MUS MUSCULUS C57BL6 strain Figure 23. MUS MUSCULUS chromosome database Home Page Figure 24. X chromosome database webpage of MUS MUSCULUS C57BL6 strain

Contents

S.No.
1. 2. 3. Introduction Review of literature

Title

Page No.
1 4 7

Materials and Methods 3.1 Web based tools used for characterization 3.2 Methodology

4. 5. 6.

Results Discussion References

16 26 I

Abstract
Protein characterization plays an important role in determining the structural as well as the functional aspects of the protein. It helps us in providing information about the biochemical mechanism of proteins at an atomic level as well as aids in the quality assessment of the protein characterized. In this project, we consider a strain C57BL/6 obtained from Mus musculus. The uncharacterized proteins lack a specified function. We, therefore try to identify the sequences, segregate the uncharacterized protein from the characterized ones and determine its structure and functions with the help of online tools. This in silico approach aids in the Proteome Projects; as it can serve as a resource for comparison of proteomes across species. As example a database of MUS MUSCULUS (strain C57BL/6) sex chromosomes uncharacterized proteins is created with predicted structure (3D) and functions which is freely available for download, review, refinement and update via: https://sites.google.com/site/musmusculuschromosomedatabase/