AmpliBASE MT™: A Mycobacterium tuberculosis diversity knowledgebase

Ahmed A. Majeed; Niyaz Ahmed; K. Rajender Rao; S. Ghousunnissa; Farhana Kauser; Buddhaditta Bose; H. A. Nagarajaram; V. M. Katoch; Debby V. Cousins; Leonardo A. Sechi; Robert H. Gilman; Seyed E. Hasnain

doi:10.1093/bioinformatics/bth051

AmpliBASE MT™: A Mycobacterium tuberculosis diversity knowledgebase

Ahmed A. Majeed, Niyaz Ahmed, K. Rajender Rao, S. Ghousunnissa, Farhana Kauser, Buddhaditta Bose, H. A. Nagarajaram, V. M. Katoch, Debby V. Cousins, Leonardo A. Sechi, Robert H. Gilman, Seyed E. Hasnain

Bloomberg School of Public Health

Research output: Contribution to journal › Article › peer-review

17 Scopus citations

Abstract

Summary: AmpliBASE MT™ is an online databank of high-resolution DNA fingerprints representing fluorescent amplified fragment length polymorphism (FAFLP) profiles or amplitypes developed for the Mycobacterium tuberculosis complex strains from 48 different countries. AmpliBASE MT™ is based on a relational database management system 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 along with the FAFLP records that will give the overall comparisons. Being the first of its kind, AmpliBASE MT™ 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.

Original language	English (US)
Pages (from-to)	989-992
Number of pages	4
Journal	Bioinformatics
Volume	20
Issue number	6
DOIs	https://doi.org/10.1093/bioinformatics/bth051
State	Published - Apr 12 2004

ASJC Scopus subject areas

Statistics and Probability
Biochemistry
Molecular Biology
Computer Science Applications
Computational Theory and Mathematics
Computational Mathematics

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10.1093/bioinformatics/bth051

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title = "AmpliBASE MT{\texttrademark}: A Mycobacterium tuberculosis diversity knowledgebase",

abstract = "Summary: AmpliBASE MT{\texttrademark} is an online databank of high-resolution DNA fingerprints representing fluorescent amplified fragment length polymorphism (FAFLP) profiles or amplitypes developed for the Mycobacterium tuberculosis complex strains from 48 different countries. AmpliBASE MT{\texttrademark} is based on a relational database management system 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 along with the FAFLP records that will give the overall comparisons. Being the first of its kind, AmpliBASE MT{\texttrademark} 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.",

author = "Majeed, {Ahmed A.} and Niyaz Ahmed and Rao, {K. Rajender} and S. Ghousunnissa and Farhana Kauser and Buddhaditta Bose and Nagarajaram, {H. A.} and Katoch, {V. M.} and Cousins, {Debby V.} and Sechi, {Leonardo A.} and Gilman, {Robert H.} and Hasnain, {Seyed E.}",

note = "Funding Information: Financial support from WHO/TDR, International Society for Infectious Diseases (ISID), and core grants to CDFD from the Department of Biotechnology, Government of India is acknowledged. We thank D. van Soolingen and Kristin Kremer for providing a collection of DNA samples from internationally accepted reference strains. Support received from CDFD Bioinformatics team (Ranjit Kumar Gundu, Phani Prasad and Prashanthi) in implementation and hosting the database is acknowledged with thanks. We thank Yogesh Prasad (Applied Biosystems/Labindia) for helpful suggestions and discussions.",

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AU - Majeed, Ahmed A.

AU - Ahmed, Niyaz

AU - Rao, K. Rajender

AU - Ghousunnissa, S.

AU - Kauser, Farhana

AU - Bose, Buddhaditta

AU - Nagarajaram, H. A.

AU - Katoch, V. M.

AU - Cousins, Debby V.

AU - Sechi, Leonardo A.

AU - Gilman, Robert H.

AU - Hasnain, Seyed E.

N1 - Funding Information: Financial support from WHO/TDR, International Society for Infectious Diseases (ISID), and core grants to CDFD from the Department of Biotechnology, Government of India is acknowledged. We thank D. van Soolingen and Kristin Kremer for providing a collection of DNA samples from internationally accepted reference strains. Support received from CDFD Bioinformatics team (Ranjit Kumar Gundu, Phani Prasad and Prashanthi) in implementation and hosting the database is acknowledged with thanks. We thank Yogesh Prasad (Applied Biosystems/Labindia) for helpful suggestions and discussions.

PY - 2004/4/12

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N2 - Summary: AmpliBASE MT™ is an online databank of high-resolution DNA fingerprints representing fluorescent amplified fragment length polymorphism (FAFLP) profiles or amplitypes developed for the Mycobacterium tuberculosis complex strains from 48 different countries. AmpliBASE MT™ is based on a relational database management system 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 along with the FAFLP records that will give the overall comparisons. Being the first of its kind, AmpliBASE MT™ 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.

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AmpliBASE MT™: A Mycobacterium tuberculosis diversity knowledgebase

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