About the Bioinformatics Centre

The Bioinformatics Infrastructure Facility in the college was set up in Dec 2006. The facility now has 2 servers, 10 PC’s, a network printer, scanner and copier. A dedicated internet connection with the speed of 2Mbps has been provided to the facility. The Facility procured Bioinformatics software SYSTAT12, FlexX, FlexPharm, Corina_F, Amber 11, Matlab, and academic licensed software Dock 6.2, Modeller v 9.0, Haddock. Training programs have been conducted frequently. The facility also conducted a two month certificate course for M.Sc. Students. Six studentships and four traineeships have been offered to students of Bioinformatics background. Access for browsing for research material is being provided for M.Phil, Ph.D & Post doc Students. The facility is being used by the faculty of our college and neighboring colleges.
As of now, 346 students and 53 faculties have benefited by the Bioinformatics course and workshops conducted by the center. For more information and database access visit
Area of specialization: Microbiology, Structural Bioinformatics, Proteomics and Computational Biology, docking and Phylogenetic studies
    • To establish BIF to support the teaching activities of Biology and its allied areas of the host institute in particular and the neighboring institutions in general.
    • To build up information resources, prepare databases of interest to its users and to develop relevant information handling tools and techniques.
    • To access information requirements, organize creation of necessary infrastructure and to provide information and computer support services to the users.
    • To establish linkages with BTISnet of DBT for sharing information Resources and users.
    • To organize Training/Workshops for familiarizing the applications of Bioinformatics in Biology teaching and learning activities.
Current area of research

Structure prediction of airborne fungal allergic proteins

Exposure to fungi, particularly in water damaged indoor environments, has been thought to exacerbate a number of adverse health effects, ranging from subjective symptoms such as fatigue, cognitive difficulties or memory loss to more definable diseases such as allergy, asthma and hypersensitivity pneumonitis. Understanding the role of fungal exposure in these environments has been limited by methodological difficulties in enumerating and identifying various fungal components in environmental samples
Airborne fungal spores occur widely and often in far greater concentrations than pollen grains. Immunoglobulin E-specific antigens (allergens) on airborne fungal spores induce type I hypersensitivity (allergic) respiratory reactions in sensitized atopic subjects, causing rhinitis and/or asthma. The prevalence of respiratory allergy to fungi is imprecisely known but is estimated at 20 to 30% of atopic (allergy-predisposed) individuals or up to 6% of the general population. Diagnosis and immunotherapy of allergy to fungi require well-characterized or standardized extracts that contain the relevant allergen(s) of the appropriate fungus.

Modeled structure of airborne fungal allergen Alternaria alternata

Structure comparison studies on Fungal allergic proteins of Alternaria Alternata

Allergy is seen with increasing frequency in the developing world (ISAAC, 1998). Out of over 100,000 fungal species reported, a few hundred occur as opportunists and about 100 are known to elicit mycoses in man and animals The most important allergy-causing fungal genera belonging to the ascomycota are Alternaria , Aspergillus , Bipolaris , Candida , Cladosporium, Epicoccum and Phoma, whereas Calvatia , Coprinus, Ganoderma , Pleurotus and Psilocybe are the most prominent genera of the basidiomycota
An estimated 0.5 – 1% of proteins in a given fungal proteome may be allergens. Many proteins responsible for allergic reactions have been described. Despite intensive efforts to determine what distinguishes these proteins from the other non-allergens in the same proteome, little is understood about the structural basis for allergenicity. The known fungal allergens appear to occur as functional groups such as serine proteases, heat shock proteins or thioredoxins or orthologues of proteins such as Mn superoxide dismutase or enolase.

The discovery of sequence and structure patterns can help in the understanding of relationships between sequence, structure, and function of proteins and in a bigger context help to understand the working of living organisms (Eidhammer et al., 2000). Hence, this study on the allergic proteins of Alternaria alternata will bring out the new facts about the structure patterns and their role in allergenicity.
The common region shared by more than half of the input structures

Ongoing projects

  • Integrating tools in Airborne fungal allergen database to analyze sequence and structure
  • Structure prediction of airborne fungal allergens by comparative and Ab-initio
  • Tools to analyze carbohydrate binding proteins
  • Structure prediction of taste receptor proteins



Project  title

Sankarasubramanian J

Identification of potent Inhibitor for RNA dependent RNA polymerase (RDRP) of Dengue Virus serotype-3- A Molecular docking study.

Ithayaraja M

Virtual screening of plant inhibitors for thioredoxin-like protein (TLP) of Fusarium culmorum using FlexX

Amirtha Gowri A

Insilico docking studies of Fungal allergic proteins against potent ligand  of Plant origin

Naveen P

Evolutionary analysis of fungal amylase
Phylogenetic analysis of catalase isolated from fungi



Project  title

Gayathri A

Identification of Structural patterns in airborne fungal allergic proteins

Prabha R

Promoter prediction and genome comparison of six strains of salmonella enterica

Shalini S

Promoter prediction and genome comparison of six strains of salmonella enterica

Niranjan Babu K

Database on Antifungal Plant compounds

Sankarasubramanian J

Database in Indian Earthworm

Thamizselvan I

Identification of Structural patterns in airborne fungal allergic proteins of Penicillium species


About the Institution

Maharani’s Science College for Women, Bangalore is one of prestigious Government Science College for Women in Karnataka in its 75th year of women empowerment. The institution’s pedigree can be traced back to 1938 and to the benevolent initiative of the erstwhile Maharajah of Mysore, His Highness Sri Nalvadi Krishnaraja Wodeyar. It stands as a testimony to his glorious vision of providing science education exclusively to girls. The institution has since then taken giant strides forward to become a popular choice of the milieu, aspiring to get quality education at nominal cost.  The college with its aesthetically designed heritage building is ensconced amidst a sprawling campus of over 11. 4 acres and is located in close proximity to Vidhana Soudha - the seat of power in the state. The college has earned recognition from various statutory bodies. The institution has obtained 2(f) and 12 (b) tag of the UGC and has been re accredited by NAAC with a CGPA of 2.78 in 2009.

Achievements at a glance
  • 9 workshops on Basic Bioinformatics have been conducted and about 193 students participated
  • 13 Two months course on Bioinformatics have been  conducted benefitting around  281
  • M.Phil dissertation- An assessment of airborne fungal allergens in indoor environment: A Bioinformatics approach has been completed
Databases/applications developed

AFAD (Airborne Fungal Allergen Database)

The AFAD contains an extensive collection of airborne fungal allergen sequences from Ascomycota, Basidiomycota and Zygomycota. The data have been extracted from public and allergen specific databases. Only published protein sequences that do not require further analysis were collected from general databases like IUIS, Allergen Online, ALLALLERGY, NCBI, Uniprot and Allergen Index. Currently AFAD contains ~90 different protein sequences and the user interface provides diverse query types, like searching by fungal name or accession number or protein name. It also has integrated BLAST for homology search. The AFAD is publicly available at
Database on Indian Earthworms
This database gives information on earthworm species found in India. The database has a total of 518 species of Indian earthworms, of which details for around 250 species have been included. The database will be updated as and when information is obtained. We have used MYSQL as the back end to store particulars about species and designed the database by the PHP, which was connected through the windows operating system.
Only one database (Hungarian) is available for earthworm species, with no extra information on Indian earthworms. This database gives general information on  Introduction about earthworm, Taxonomy, Interesting Facts,Global and Indian statistics

Details of each species include  description, Morphology (Length, Diameter, Segments and Colour)
Habit and Habitat, Casting, Habit and Habitat, DNA barcoding.
This database can be accessed through

Screen shot of the search result page of the database
Infrastructure facilities
IBM server – 2 (windows -1, Redhat – 1), IBM Desktops (windows) – 10, Microsoft ISA server for proxy – 1, VS.NET Media kit – 1, MS SQL Licensed media kit – 1, MS Office professional plus 2007 – 1, Windows 2003 server std SP1 – 1, Red Hat Linux enterprise -1, HP Laser Jet Printer – 1, Toshiba E-Studio Copier – 1, HP Scan Jet Color Scanner – 1, BENQ Projector - 1.
Recent publications


Arun jyothi Mathias, PavithraK.B., Manjunatha K., 2011. “Phylogenetic Analysis of Airborne Fungal Allergens using Bioinformatics Tools”, Journal of Computational Intelligence in Bioinformatics, vol. 5(1) pp1-11.

Pavithra.K.B*., Kavitha.B., Prabha.R, Rajasekaran.G., “Identification of potent an- tifungal plant compound against alkaline proteinase of Aspergillus fumigatus” accepted in International Journal of Fundamental and Applied Sciences.

Faculty members

Dr.Kavitha B
Head of the Department (UG & PG),
Department of Microbiology,
Maharani’s Science College for Women,
Bangalore -560001.
Phone: +91-080-22371416 Email:,


Dr. Arun Jyothi Mathias
Associate Professor
Department of Microbiology,
Maharani’s Science College for Women,
Bangalore -560001.       

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