Communication Facilities
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Database of Structure-Function Relationships on
Calcium/Calmodulin Dependent Protein Kinase II : This
database will contain available information on structure-function
relationships in CaMKII. Mutants of CaMKII will be
catalogued against their invitro biochemical properties
and physiological properties. This is under developement
with the support of Neurobiology lab.
- Online Database on Biosaftey and Radioactivity:
An online database on biosaftey and radioactivity
has been developed for students and staff.
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Lab Information System (LIS): This is a web-based
inventory system for a typical biotechnology research
laboratory. This database provides a way to collect,
maintain, present and archive information on laboratory
stocks, such as antibodies, plasmids, chemical reagents,
cell lines, records etc.
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OncoSidb - Oncogene siRNA Database: This database
contains information about siRNA molecules generated
as a result of analysis of Ras, Myc, Neu, ABL, RELA,
C-REL gene sequences using siRNA Target Finder tool.
This database enables the user to evaluate a siRNA
potential for inhibition and non-specific effect by
screening them in appropriate cell cultures.
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Tandem Repeats Database: A database of tandem repeats
from publicly available bacterial genomes, which facilitates
the identification and selection of tandem repeats.
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Curcumin Database: This database is a repository
on all available information regarding Curcumin and
is under construction.
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Softwares
Acquired: The centre has a good collection of commercial and public domain softwares covering a wide range of applications like sequence and structure analysis, molecular modeling and simulations, structure prediction and drug design.
GCG Package version 11.0 (Commercial)
Accelrys Molecular Modelling - Insight II version 2000 L (Commercial),EndNote v 5.0(Commercial)
Free/Open Softwares:- EMBOSS, Autodock, WHATIF, MODELLER ClustalW, Phylip, Cn3D, Rasmol, HMMR, Staden Package, R-statistical package, GeneDoc, Phred, Phrap & Consed package, 3d-dock suite, PyMol, Jackal etc.
Developed: The following softwares are being developed in association with various research groups:
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Genopack : This is a software package containing eight different programs, namely Allele Match Finder, Protein Sequence Generator, Consensus Sequence Generator, Position Emphasis, Format conversion, DNA Sequence Alignment and Motif Matching. This is useful for research scholars working in the area of DNA fingerprinting, SNPs etc.
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Peptide Analyzer: This is a software package is developed for the analyses of primary protein sequences. It includes Mass Spectrum Analysis, Enzyme Digestion, Hydrophobicity, Helical Wheel etc.
- Peptide Detector: This software is developed to predict specific molecular markers in sequencing products.
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SmartProject: This software features a mini accounting package designed for the needs of project management. This program integrates day to day expenses, inventory and financial accounting systems into one package. This software is built on Visual Basic with MS Access backend.
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ProTree: This programme is a SUFFIX TREE implementation for pattern searching using data structure in PERL. Here, we extend this method to search for PROSITE patterns instead of simple strings.
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SMILESIM: ‘SMILESIM’ was written in PERL to compare structure based similarity between chemical structures in SMILES format. It performs a similarity search in large Chemistry compound dataset. The comparisons of chemical structures are done at atom level, generating an output consisting of the position of matched atoms between the reference molecule and the molecule in the chemical dataset. SMILESIM can be a potential lead identification tool for various targets of pharmaceutical interest. The potential lead compounds can be estimated by similarity scoring function.
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ProScan: This is a PERL based standalone implementation of Prosite Scanning Tool. The PROSITE regular expression matching engine, implement the rules described in PROSITE, handle ambiguous sequence characters in protein databases and provide a single user interface to scan PROSITE patterns rules and profiles as well as user can also define patterns according to the prosite profile format.
Web servers developed:
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Insilico PCR Amplification Server: It is a web based program to simulate the polymerase chain reaction. You specify a target sequence and primers, and it predicts the result. It is useful for planning experiments, testing primers, displaying the list of amplicons, it position, length and sequence.
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Palindrome Analysis Server: This is a palindrome finder server. It takes a DNA sequences as input and predicts common palindromes for all sequences, displays the pattern and its position in the sequence.
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Microsatellite Find Server: This web based Microsatellite Analysis Server provides a user-friendly front end for systematically extracting the data on microsatellite repeats from genomes or a gene sequence provided for analysis. The server software will display information regarding the position of microsatellite, the frequency of occurrences, the size and number of repeating motifs.
Training and Workshop:
Organizing periodic training programmes and seminars has been an integral part of the centre. The centre has been successful in creating awareness among scientist and students of RGCB through several training programmes on different aspects of Computer Applications and Information Technology. Since its inception, the centre has been conducting National Seminars and Workshops in fields related to Bioinformatics.
- National Seminar On Bioinformatics (NSB’03) 23rd July 2003.
- National Seminar On Bioinformatics (NSB’04) 14th - 16th December 2004.
- National Conference and Workshop On Molecular Modeling (NCWMM’06) 21st -24th March 2006.
This center provides project work guidance as well as Hands on training to students undergoing B.Tech/ M.Tech/ MCA/ MSc courses from large number of Institutions/Universities.
Assistance is provided the initiate Bioinformatics activities in Central Tuber Crops Research Institute, Trivandrum includes giving assistance to develop database of their interest and installation of bioinformatics softwares for their needs.
R&D in Bioinformatics
- An In-silico approach to dock Curcumin and its analogues with proteins known to interact with Curcumin.
- Search for Non-classical Nuclear Localization Signal Proteins Similar to SMAD3.
- Building The 3 Dimensional Structure of Merlin (NF2 gene product) Through Homology Modeling Approach.
- Insilico analysis of Chalcone synthase gene family from Zingiber officinale.
Publications/Presentations:
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A paper titled "Genopack" has been accepted for the workshop on "Bioinformatics and Computational Biology" to be held in conjunction with International Conference on High Performance Computing at Hyderabad from Dec 17-20, 2003.
- A paper titled "Computational Pairwise Sequence Alignment" was presented for the workshop "Bioinformatics and Biodiversity" organized by TBGRI, TVM on Feb 26, 2004.
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Peptide Detector, a software package for the analysis of phage peptide library was published in Bioinformatics India. Vol.-2, Issue-2, April -June 2004
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Prospects of using DNA Microarray in Crop Improvement was published in Bioinformatics India. Vol.-2, Issue-2, April - June 2004.
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