RegPrecise web services interface: programmatic access to the transcriptional regulatory interactions in bacteria reconstructed by comparative genomics.

Web services application programming interface (API) was developed to provide a programmatic access to the regulatory interactions accumulated in the RegPrecise database (http://regprecise.lbl.gov), a core resource on transcriptional regulation for the microbial domain of the Department of Energy (DOE) Systems Biology Knowledgebase. RegPrecise captures and visualize regulogs, sets of genes controlled by orthologous regulators in several closely related bacterial genomes, that were reconstructed by comparative genomics. The current release of RegPrecise 2.0 includes >1400 regulogs controlled either by protein transcription factors or by conserved ribonucleic acid regulatory motifs in >250 genomes from 24 taxonomic groups of bacteria. The reference regulons accumulated in RegPrecise can serve as a basis for automatic annotation of regulatory interactions in newly sequenced genomes. The developed API provides an efficient access to the RegPrecise data by a comprehensive set of 14 web service resources. The RegPrecise web services API is freely accessible at http://regprecise.lbl.gov/RegPrecise/services.jsp with no login requirements

Modular S 4 models of lepton masses and mixing

We investigate models of charged lepton and neutrino masses and lepton mixing based on broken modular symmetry. The matter fields in these models are assumed to transform in irreducible representations of the finite modular group \u393 4 43 S 4 . We analyse the minimal scenario in which the only source of symmetry breaking is the vacuum expectation value of the modulus field. In this scenario there is no need to introduce flavon fields. Using the basis for the lowest weight modular forms found earlier, we build minimal phenomenologically viable models in which the neutrino masses are generated via the type I seesaw mechanism. While successfully accommodating charged lepton masses, neutrino mixing angles and mass-squared differences, these models predict the values of the lightest neutrino mass (i.e., the absolute neutrino mass scale), of the Dirac and Majorana CP violation (CPV) phases, as well as specific correlations between the values of the atmospheric neutrino mixing parameter sin 2 \u3b8 23 and i) the Dirac CPV phase \u3b4, ii) the sum of the neutrino masses, and iii) the effective Majorana mass in neutrinoless double beta decay. We consider also the case of residual symmetries \u2124 3ST and \u2124 2S respectively in the charged lepton and neutrino sectors, corresponding to specific vacuum expectation values of the modulus

Modular S 4 models of lepton masses and mixing

We investigate models of charged lepton and neutrino masses and lepton mixing based on broken modular symmetry. The matter fields in these models are assumed to transform in irreducible representations of the finite modular group Γ 4 ≃ S 4 . We analyse the minimal scenario in which the only source of symmetry breaking is the vacuum expectation value of the modulus field. In this scenario there is no need to introduce flavon fields. Using the basis for the lowest weight modular forms found earlier, we build minimal phenomenologically viable models in which the neutrino masses are generated via the type I seesaw mechanism. While successfully accommodating charged lepton masses, neutrino mixing angles and mass-squared differences, these models predict the values of the lightest neutrino mass (i.e., the absolute neutrino mass scale), of the Dirac and Majorana CP violation (CPV) phases, as well as specific correlations between the values of the atmospheric neutrino mixing parameter sin 2 θ 23 and i) the Dirac CPV phase δ, ii) the sum of the neutrino masses, and iii) the effective Majorana mass in neutrinoless double beta decay. We consider also the case of residual symmetries ℤ 3ST and ℤ 2S respectively in the charged lepton and neutrino sectors, corresponding to specific vacuum expectation values of the modulus

RegPredict: an integrated system for regulon inference in prokaryotes by comparative genomics approach

RegPredict web server is designed to provide comparative genomics tools for reconstruction and analysis of microbial regulons using comparative genomics approach. The server allows the user to rapidly generate reference sets of regulons and regulatory motif profiles in a group of prokaryotic genomes. The new concept of a cluster of co-regulated orthologous operons allows the user to distribute the analysis of large regulons and to perform the comparative analysis of multiple clusters independently. Two major workflows currently implemented in RegPredict are: (i) regulon reconstruction for a known regulatory motif and (ii) ab initio inference of a novel regulon using several scenarios for the generation of starting gene sets. RegPredict provides a comprehensive collection of manually curated positional weight matrices of regulatory motifs. It is based on genomic sequences, ortholog and operon predictions from the MicrobesOnline. An interactive web interface of RegPredict integrates and presents diverse genomic and functional information about the candidate regulon members from several web resources. RegPredict is freely accessible at http://regpredict.lbl.gov

MicrobesOnline: an integrated portal for comparative and functional genomics

Since 2003, MicrobesOnline (http://www.microbesonline.org) has been providing a community resource for comparative and functional genome analysis. The portal includes over 1000 complete genomes of bacteria, archaea and fungi and thousands of expression microarrays from diverse organisms ranging from model organisms such as Escherichia coli and Saccharomyces cerevisiae to environmental microbes such as Desulfovibrio vulgaris and Shewanella oneidensis. To assist in annotating genes and in reconstructing their evolutionary history, MicrobesOnline includes a comparative genome browser based on phylogenetic trees for every gene family as well as a species tree. To identify co-regulated genes, MicrobesOnline can search for genes based on their expression profile, and provides tools for identifying regulatory motifs and seeing if they are conserved. MicrobesOnline also includes fast phylogenetic profile searches, comparative views of metabolic pathways, operon predictions, a workbench for sequence analysis and integration with RegTransBase and other microbial genome resources. The next update of MicrobesOnline will contain significant new functionality, including comparative analysis of metagenomic sequence data. Programmatic access to the database, along with source code and documentation, is available at http://microbesonline.org/programmers.html.United States. Dept. of Energy (Genomics: GTL program (grant DE-AC02-05CH11231)

ATGC: a database of orthologous genes from closely related prokaryotic genomes and a research platform for microevolution of prokaryotes

The database of Alignable Tight Genomic Clusters (ATGCs) consists of closely related genomes of archaea and bacteria, and is a resource for research into prokaryotic microevolution. Construction of a data set with appropriate characteristics is a major hurdle for this type of studies. With the current rate of genome sequencing, it is difficult to follow the progress of the field and to determine which of the available genome sets meet the requirements of a given research project, in particular, with respect to the minimum and maximum levels of similarity between the included genomes. Additionally, extraction of specific content, such as genomic alignments or families of orthologs, from a selected set of genomes is a complicated and time-consuming process. The database addresses these problems by providing an intuitive and efficient web interface to browse precomputed ATGCs, select appropriate ones and access ATGC-derived data such as multiple alignments of orthologous proteins, matrices of pairwise intergenomic distances based on genome-wide analysis of synonymous and nonsynonymous substitution rates and others. The ATGC database will be regularly updated following new releases of the NCBI RefSeq. The database is hosted by the Genomics Division at Lawrence Berkeley National laboratory and is publicly available at http://atgc.lbl.go