Please add to this list of institutes which provide a PhD in Bioinformatics (specifically) so that a comprehensive list can be prepared.
Allahabad University
Bharathidasan University, TamilNadu
Banasthali University, Rajasthan
Bose Institute, Kolkata
Calcutta University
Central University of South Bihar, Gaya
Dr. D.Y. Patil Biotechnology and Bioinformatics Institute, Pune
IBAB, Bangalore
IIIT Allahabad
IIIT Delhi
IIIT Hyderabad
Jaypee University of Information Technology, Solan, Himachal Pradesh
Karunya University, Tamil Nadu
National Institute of Technology, Bhopal
Pondicherry University
Sastra University,Tamil Nadu
SHUATS, Allahabad
WBUT, Salt Lake, Kolkata
Allahabad University
Bharathidasan University, TamilNadu
Banasthali University, Rajasthan
Bose Institute, Kolkata
Calcutta University
Central University of South Bihar, Gaya
Dr. D.Y. Patil Biotechnology and Bioinformatics Institute, Pune
IBAB, Bangalore
IIIT Allahabad
IIIT Delhi
IIIT Hyderabad
Jaypee University of Information Technology, Solan, Himachal Pradesh
Karunya University, Tamil Nadu
National Institute of Technology, Bhopal
Pondicherry University
Sastra University,Tamil Nadu
SHUATS, Allahabad
WBUT, Salt Lake, Kolkata