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Bioinformatics Advance Access published online on February 5, 2004
Bioinformatics, doi:10.1093/bioinformatics/bth051
Bioinformatics © Oxford University Press 2004; all rights reserved
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Received January 2, 2003
Revised November 12, 2003
Accepted November 12, 2003

Applications note

AmpliBASE MTTM: a Mycobacterium tuberculosis diversity knowledgebase

Ahmed A. Majeed 1, Niyaz Ahmed 1, K. Rajender Rao 1, S. Ghousunnissa 1, Farhana Kausar 1, Buddhaditta Bose 1, H. A. Nagarajaram 1, V. M. Katoch 2, Debby V. Cousins 3, Leonardo A. Sechi 4, Robert H. Gilman 5, Seyed E. Hasnain 6*

1 Centre for DNA Fingerprinting and Diagnostics, Nacharam, Hyderabad 500 076, India
2 National Mycobacterial Repository Centre, Central JALMA Institute for Leprosy (ICMR), Agra 282001, India
3 Australian Reference Laboratory for Bovine Tuberculosis, Agriculture Western Australia, South Perth, Australia
4 Department of Biomedical Sciences, University of Sassari, Sardinia, Italy
5 The Johns Hopkins Bloomberg School of Public Health and Hygiene, Baltimore, USA
6 Centre for DNA Fingerprinting and Diagnostics, Nacharam, Hyderabad 500 076, India; Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore 560064, India

* To whom correspondence should be addressed. E-mail: amplibas{at}cdfd.org.in.


  Abstract

Summary: AmpliBASE MTTM is an online databank of high-resolution DNA fingerprints representing fluorescent amplified fragment length polymorphism (FAFLP) profiles or amplitypes developed for the M. tuberculosis complex strains from 48 different countries. AmpliBASE MTTM is based on a relational database management system (RDBMS) that is hyperlinked to visualize genotyping results in the form of DNA fingerprint images for individual strains. A flexible search system based on systematic comparisons of fragment sizes in base pairs allows inter-laboratory comparison of FAFLP profiles. Besides this, the database also displays previously published data on IS6110 profiles, spoligotypes, MIRU-VNTRs, and large sequence polymorphisms alongwith the FAFLP records that will give the overall comparisons. Being the first of its kind, AmpliBASE MTTM is expected to be a very helpful tool in strengthening the concept of ‘geographic genomics’ and will be very helpful to molecular epidemiologists and those interested in diagnostic development for tuberculosis.

Availability: http://210.212.212.4/index.html


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