Jomuna V. Choudhuri

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The repetitive structure of genomic DNA holds many secrets to be discovered. A systematic study of repetitive DNA on a genomic or inter-genomic scale requires extensive algorithmic support. The REPuter program described herein was designed to serve as a fundamental tool in such studies. Efficient and complete detection of various types of repeats is(More)
The release of the 1000th complete microbial genome will occur in the next two to three years. In anticipation of this milestone, the Fellowship for Interpretation of Genomes (FIG) launched the Project to Annotate 1000 Genomes. The project is built around the principle that the key to improved accuracy in high-throughput annotation technology is to have(More)
Members of the Bacteroidetes, formerly known as the Cytophaga-Flavobacteria-Bacteroides (CFB) phylum, are among the major taxa of marine heterotrophic bacterioplankton frequently found on macroscopic organic matter particles (marine snow). In addition, they have been shown to also represent a significant part of free-living microbial assemblages in(More)
The genus Sorangium synthesizes approximately half of the secondary metabolites isolated from myxobacteria, including the anti-cancer metabolite epothilone. We report the complete genome sequence of the model Sorangium strain S. cellulosum So ce56, which produces several natural products and has morphological and physiological properties typical of the(More)
SUMMARY Genalyzer is a software tool designed for the interactive visualization of sequence matches between DNA or protein sequences. It provides visualizations on different levels of granularity, from complete overviews via zoomed regions to alignments of particular matching substrings. Genalyzer can efficiently handle very large datasets, allowing to(More)
Bordetella petrii is the only environmental species hitherto found among the otherwise host-restricted and pathogenic members of the genus Bordetella. Phylogenetically, it connects the pathogenic Bordetellae and environmental bacteria of the genera Achromobacter and Alcaligenes, which are opportunistic pathogens. B. petrii strains have been isolated from(More)
Background: Bordetella petrii is the only environmental species hitherto found among the otherwise host-restricted and pathogenic members of the genus Bordetella. Phylogenetically, it connects the pathogenic Bordetellae and environmental bacteria of the genera Achromobacter and Alcaligenes, which are opportunistic pathogens. B. petrii strains have been(More)
The repeatitive pattern of genomic DNA reveals much about the structure and organization of genomes. REPuter is a bioinformatics tool that efficiently finds repeatitive substrings in large genomic sequences. The identification of repeats enables a wide range of biological interpretations. Here we describe how this single software is applied to many(More)
Susanne Schneiker1,17, Olena Perlova2,17, Olaf Kaiser1, Klaus Gerth3, Aysel Alici1, Matthias O Altmeyer2, Daniela Bartels4, Thomas Bekel4, Stefan Beyer3, Edna Bode2, Helge B Bode2, Christoph J Bolten5, Jomuna V Choudhuri4, Sabrina Doss6, Yasser A Elnakady2, Bettina Frank2, Lars Gaigalat1, Alexander Goesmann3, Carolin Groeger6, Frank Gross2, Lars Jelsbak7,(More)