Bioinformatics Centre, Svatribai Phule Pune University

Wellcome to Cloud Platform!

Bioinformatics Centre at the Savitribai Phule Pune University (SPPU, formerly University of Pune) was established in 1987 as a Distributed Information Centre (DIC) under the Biotechnology Information System Network (BTISNET) established by the Department of Biotechnology (DBT), Govt. of India. Ever since its inception, the Centre has made perceptible impact towards the growth of the discipline of Bioinformatics at the national and international levels. As a culmination of this, the Centre is conferred with the status of the Centre of Excellence (CoE) in Bioinformatics by the DBT (2002 - till date). It also has a distinction of being recognised as the Centre of Excellence (CoE) in Bioinformatics by the Department of Electronics & Information Technology (DeitY), Govt. of India during 2008-2013. The centre is equipped with the-state-of-the-art infrastructure and a specialised library. The faculty & the students at the Centre are engaged in carrying out cutting-edge research in various areas of Bioinformatics with a special focus on ViroInformatics and Structural Bioinformatics. The mission of the Bioinformatics Centre at SPPU has been and continues to be a nationally acclaimed and internationally recognised premier institution of higher education and research in Bioinformatics and Computational Biology.
The Centre is known for its contributions in R&D and has developed several algorithms, servers and databases which are extensively used by the scientific community. Some of these indigenous algorithms and databases are the firsts in respective categories and have made a significant impact nationally and internationally. The centre has an impressive record of publications, citations and usage statistics for its servers and databases.
The Centre is happy to announce launch of the cloud platform to host the databases and servers and profusely acknowledges Centre for Information & Network Security (CINS), Savitribai Phule Pune University for coming forward to develop cloud and related facilities dedicated to Bioinformatics.With Bioinformatics Centre, CINS@SPPU is also successfully launching cloud environment for the first time on SPPU campus!

Databases

AllerBase

AllerBase is a comprehensive knowledgebase of allergens and allergen related data. The database provides an in depth coverage of allergens and related data with cross-references to primary, immunological and allergen databases.
Publication:

Kiran Kadam, Rajiv Karbhal, V. K. Jayaraman, Sangeeta Sawant, Urmila Kulkarni-Kale; AllerBase: a comprehensive allergen knowledgebase, Database, Volume 2017, 1 January 2017, bax066.

Link: https://bioinfo.unipune.ac.in/AllerBase/Home.html

Antigen Antibody Interaction Database (AgAbDb)

AgAbDb, a derived knowledge base archives molecular interactions of protein and peptide antigens characterized by co-crystal structures. The interactions are characterized using AAIF (Antigen-Antibody Interaction Finder) developed in-house.
Publication:

Ghate AD, Bhagwat BU, Bhosle SG, Gadepalli SM, Kulkarni-Kale UD (2007). Characterization of antibody-binding sites on proteins: development of a knowledgebase and its applications in improving epitope prediction. Protein Pept. Lett;14(6):531-5.
Kulkarni-Kale U, Raskar-Renuse S, Natekar-Kalantre G & Saxena SA. (2014). Antigen-Antibody Interaction Database (AgAbDb): A compendium of antigen-antibody interactions in the book Immunoinformatics, Second Edition Eds: De RK & Tomar N, published by Springer Printer & Business Media. Methods in molecular biology (Clifton, N.J.) 01/2014; 1184:149-64.

Link: http://196.1.114.46:8080/agabdb2/home.jsp

Data Extraction

BioDb Extractor

BioDB Extractor (BDE) provides customized search and extraction utilities for widely used Bioinformatics databases such as ENA (EMBL-Bank), UniprotKB, PDB, and KEGG through web-based user interface. Current version supports 26 utilities are supported.
Publication:

Karbhal R, Sawant S, Kulkarni-Kale U. BioDB extractor: customized data extraction system for commonly used bioinformatics databases. BioData Min. 2015 Oct 28;8:31.

Link: https://bioinfo.unipune.ac.in/BioDB/Home.html

Web Servers

Aeromons MLSTyper

MLSTyper helps to identify the Aeromonas species by Multiple-locus Sequence Typing (MLST) method using novel alignment-free method based on Return Time Distribution (RTD) developed in-house.
Publication: Manuscript under preparation. Link: http://bioinfo.net.in/aeromonas/homepage.html

Dengue Subtyper

Dengue Subtyper server assigns serotype/genotype to query sequence(s) using an alignment-free method based on Return Time Distribution (RTD), which is developed in-house. Typing of Dengue viruses is carried out using whole genome sequencs.
Publication:

Kolekar P, Kale M, Kulkarni-Kale U. Alignment-free distance measure based on return time distribution for sequence analysis: Applications to clustering, molecular phylogeny and subtyping. Mol Phylogenet Evol. 2012; 65(2):510-22.

Link: https://bioinfo.unipune.ac.in/Dengue/home.html

HRV Typer

This server assigns serotype to query sequence(s) of VP1 protein of Human rhinoviruses A, B & C using RTD-based approach. Server accepts nucleotide or protein sequence of VP1 and computes return times of di-peptides (k = 2) to assign serotypes. The RV-Typer performs with 100% sensitivity and specificity.
Publication:

Kolekar PS, Waman VP, Kale MM, Kulkarni-Kale U. RV-Typer: A Web Server forTyping of Rhinoviruses Using Alignment-Free Approach. PLoS One. 2016. 11(2):e0149350.

Link: https://bioinfo.unipune.ac.in/RV-Typer/home.html

IDV Typer

Infulenza D virus (IDV) is currently classified into lineages based on the Hemagglutinin-Esterase Fusion (HEF) gene. This server assigns lineage to the IDV isolates based on the HEF query sequence(s) using the alignment-free method based on Return Time Distribution (RTD).
Publication:

Limaye S, Shelke A, Kale MM, Kulkarni-Kale U, Kuchipudi SV. IDV Typer: An Automated Tool for Lineage Typing of Influenza D Viruses Based on Return Time Distribution. Viruses. 2024 Feb 28;16(3):373. doi: 10.3390/v16030373.

Link: https://bioinfo.unipune.ac.in/IDV/home.html

MuV genotyping server

Genotyping of Mumps is carried out using SH gene sequences. Mumps Virus (MuV) genotyping server assigns genotype to query sequence(s) of small hydrophobic (SH) gene. The server uses two conventional methods viz., BLAST, molecular phylogeny analysis (MPA) and a novel method based on Return Time Distribution (RTD), which is developed in-house.
Publication:

Kolekar, P. S., Kale M. M. and Kulkarni-Kale, U. Genotyping of Mumps viruses based on SH gene: Development of a server using alignment-free and alignment-based methods. Immunome Research (2011). 7:3:4

Link: https://bioinfo.unipune.ac.in/Muv1.1/homepage.html

RTD Phylogeny

RTD Phylogeny server is an implementation of Return Time Distribution (RTD) based alignment-free approach developed in house for phylogeny of genomic sequences. While most of the alignment-free methods use frequencies of k-mers in genomic sequences, RTD-based method utilises relative occurrence or 'return times' of k-mers to summarise their compositions in the form of RTDs.
Publication:

Kolekar P, Kale M, Kulkarni-Kale U. Alignment-free distance measure based on return time distribution for sequence analysis: Applications to clustering, molecular phylogeny and subtyping. Mol Phylogenet Evol. 2012; 65(2):510-22.
Kolekar, P. S., Kale M. M. and Kulkarni-Kale, U., Inter-Arrival Time Inspired Algorithm and its Application in Clustering and Molecular Phylogeny", AIP Conference Proceedings 2010. 1298(1):307-312. ISBN 978-0-7354-0854-8.

Link: https://bioinfo.unipune.ac.in/RTD/home.html

WNV Typer

WNV Typer has been developed to predict lineage/genotype of West Nile viruses using the complete coding sequences as an input. The server uses alignment-free approach based on RTD at back-end.
Publication:

Kolekar P, Hake N, Kale M, Kulkarni-Kale U. WNVTyper: a server for genotyping of West Nile viruses using an alignment-free method based ona return time distribution. J Virol Methods. 2014. 198:41-55.

Link: https://bioinfo.unipune.ac.in/WNV/homepage.html

IRESPred

IRESPred is a Support Vector Machine (SVM) based computational tool to predict the presence of Internal Ribosome Entry Site (IRES) in viral and cellular 5'UTR sequences.
Publication:

Kolekar, P., et al. IRESPred: Web Server for Prediction of Cellular and Viral Internal Ribosome Entry Site (IRES). Sci Rep 2016;6:27436.

Link: https://bioinfo.unipune.ac.in/IRESPred/home.html

ConformationalEpitope Prediction (CEP) Server

CEP predicts both, linear and conformational epitopes of protein antigens using 3D structure as an input. It is the first algorithm that was developed to predict conformational epitopesusing accessibility and distance-based cut-off criteria.
Publication:

Kulkarni-Kale U, Bhosle S, Kolaskar AS. CEP: a conformational epitope prediction server. Nucleic Acids Res. 2005. 33(Web Server issue):W168-71.
Kolaskar AS, Kulkarni-Kale U. Prediction of three-dimensional structure and mapping of conformational epitopes of envelope glycoprotein of Japanese encephalitis virus. Virology. 1999. 261(1):31-42.

Link: http://bioinfo.net.in/wnv/homepage.html

ProtFract

ProtFract analyses interior and exterior of proteins using fractals. It offers two classes of broad services: services meant for calculating many protein interior fractal-properties and services meant for calculating protein exterior fractal-properties using 3D coordinates as a starting point. ProtFract calculates the self-similarity in inhomogeneous distributions of mass, hydrophobicity and polarizability with fractal dimension (FD).
Publication:

Banerji A, Ghosh I. Fractal symmetry of protein interior: what have we learned? Cell Mol Life Sci. 2011 Aug;68(16):2711-37.

Link: http://196.1.114.49/fract/

Postal Address:
Bioinformatics Centre,
Savitribai Phule Pune University (Formerly University of Pune),
Pune 411 007,
Maharashtra, India.
Telephone +91 20 25692039, 25690195
Fax +91 20 25690087

E-mail: bioinfosppu@gmail.com