A web server that performs automated, in-depth annotation of bacterial genomic (chromosomal and plasmid) sequences. BASys uses more than 30 programs to determine nearly 60 annotation subfields for each gene, including gene/protein name, GO function, COG function, possible paralogues and orthologues, molecular weight, isoelectric point, operon structure, subcellular localization, signal peptides, transmembrane regions, reactions, and pathways. The textual annotations and images that are provided by BASys can be generated in approximately 16 hours for an average bacterial chromosome (5 Megabases. 5000 genes), or approximately 350 coding regions per hour.
Allows users to submit known or experimentally determined binding sites of a regulatory protein as ungapped multiple sequence alignments. PredictRegulon is a web server tool for genome-wide prediction of potential binding sites and target operons of a regulatory protein for which few experimentally identified binding sites are known. This technique could utilize the available experimental data on binding sites of transcription regulatory proteins from various bacterial species for identification of regulons in phylogenetically related species.
Allows users to identify new protein binding sites on fully sequenced prokaryotic genomes. FITBAR is a real-time position-specific scoring matrix (PSSM) scanning web tool for completely sequenced prokaryotic genomes. It provides two algorithms for the detection of new binding sites in combination with two methods to calculate their P-values. It aims to assist the experimentalist with the discovery and characterization of new prokaryotic regulons.
Provides a prediction method for transcription units (TU prediction) in the bacterial whole genome. TREBAX uses integrated analysis of microarray and DNA sequence data to identify unknown TUs and detect internal operons in the known operons. Moreover, by modifying the respective input format, the software can also be employed to analyze different data.
Identifies operons and conserved gene arrays in bacterial datasets. SLING exploits one of the conserved genes within the array to detect the linked genes that appear in a rule-defined proximity. This application leans on a single gene to perform its search function and can be used to discover novel genes by looking directly at the partner genes identified or, indirectly, by building hidden Markov models (HMMs) profiles of newly identified partner genes.
Uses transcriptomic features extracted from RNA-seq transcriptome profiles to develop ensemble classifiers for condition-dependent operon predictions. The CONDOP package provides a deeper insight into RNA-seq data analysis and allows scientists to highlight the operon organization in the context of transcriptional regulation with a few lines of code.