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Defining the gene products that play an essential role in an organism's functional repertoire is vital to understanding the system level organization of living cells. We used a genetic footprinting technique for a genome-wide assessment of genes required for robust aerobic growth of Escherichia coli in rich media. We identified 620 genes as essential and(More)
Analysis of a newly sequenced bacterial genome starts with identification of protein-coding genes. Functional assignment of proteins requires the exact knowledge of protein N-termini. We present a new program ORPHEUS that identifies candidate genes and accurately predicts gene starts. The analysis starts with a database similarity search and identification(More)
Concepts of orthology and paralogy are become increasingly important as whole-genome comparison allows their identification in complete genomes. Functional specificity of proteins is assumed to be conserved among orthologs and is different among paralogs. We used this assumption to identify residues which determine specificity of protein-DNA and(More)
An important and still unsolved problem in gene prediction is designing an algorithm that not only predicts genes but estimates the quality of individual predictions as well. Since experimental biologists are interested mainly in the reliability of individual predictions (rather than in the average reliability of an algorithm) we attempted to develop a gene(More)
Bacterial response to nitric oxide (NO) is of major importance since NO is an obligatory intermediate of the nitrogen cycle. Transcriptional regulation of the dissimilatory nitric oxides metabolism in bacteria is diverse and involves FNR-like transcription factors HcpR, DNR, and NnrR; two-component systems NarXL and NarQP; NO-responsive activator NorR; and(More)
The RegPrecise database (http://regprecise.lbl.gov) was developed for capturing, visualization and analysis of predicted transcription factor regulons in prokaryotes that were reconstructed and manually curated by utilizing the comparative genomic approach. A significant number of high-quality inferences of transcriptional regulatory interactions have been(More)
Computational comparative techniques were applied to analysis of the aromatic amino acid regulons in gamma-proteobacteria. This resulted in characterization of the TrpR and TyrR regulons in the genomes of Yersinia pestis, Haemophilus influenzae, Vibrio cholerae and other bacteria and identification of new members of the PhhR regulon in the genome of(More)
Riboswitches are structures that form in mRNA and regulate gene expression in bacteria. Unlike other known RNA regulatory structures, they are directly bound by small ligands. The mechanism by which gene expression is regulated involves the formation of alternative structures that, in the repressing conformation, cause premature termination of transcription(More)
Alternative splicing has recently emerged as a major mechanism of generating protein diversity in higher eukaryotes. We compared alternative splicing isoforms of 166 pairs of orthologous human and mouse genes. As the mRNA and EST libraries of human and mouse are not complete and thus cannot be compared directly, we instead analyzed whether known cassette(More)
RegTransBase is a manually curated database of regulatory interactions in prokaryotes that captures the knowledge in public scientific literature using a controlled vocabulary. Although several databases describing interactions between regulatory proteins and their binding sites are already being maintained, they either focus mostly on the model organisms(More)