Absynte is a web-based service designed to display local syntenies in completely sequenced prokaryotic chromosomes. The genomic contexts are determined with a multiple center star clustering topology on the basis of a user-provided protein sequence and all (or a set of) chromosomes from the publicly available archaeal and bacterial genomes. The results consist in a dynamic web page where a consistent color coding permits a rapid visual evaluation of the relative positioning of genes with similar sequences within the synteny. Each gene composing the synteny can be further queried interactively using either local or remote databases. Absynte results can be exported in .CSV or high resolution .PDF formats for printing, archival, further editing or publication purposes. Performance, real-time computation, user-friendliness and daily database updates constitute the principal advantages of Absynte over similar web services.

Reference: Despalins, A., Marsit, S. & Oberto, J. Bioinformatics (2011); doi: 10.1093/bioinformatics/BTR473
[Abstract] [PDF article]

FITBAR is a web service designed to identify new protein binding sites on fully sequenced prokaryotic genomes. This tool consists in a workbench where the significance of the predictions can be compared using different statistical methods, a feature not found in existing resources. The Local Markov Model and the Compound Importance Sampling algorithms have been implemented to compute the P-value of newly discovered binding sites. In addition, FITBAR provides two optimized genomic scanning algorithms using either log-odds or entropy-weighted position-specific scoring matrices. Other significant features include the production of a detailed genomic context map for each detected binding site and the export of the search results in spreadsheet and portable document formats. FITBAR discovery of a high affinity Escherichia coli NagC binding site was validated experimentally in vitro as well as in vivo and published.

Reference: Oberto, J. BMC Bioinformatics (2010) 11:554doi:10.1186/1471-2105-11-554
[Abstract] [PDF article]

BAGET is a web service designed to facilitate extraction, by molecular geneticists and phylogeneticists, of specific gene and protein sequences from completely determined prokaryotic genomes. Upon selection of a particular prokaryotic organism and gene, two levels of visual gene context information are provided on a single dynamic page: i) a graphical representation of a user defined portion of the chromosome centered on the gene of interest and ii) the DNA sequence of the query gene, of the immediate neighboring genes and the intergenic regions each identified by a consistent color code. The aminoacid sequence is provided for protein-coding query genes. Query results can be exported as a rich text format (RTF) word processor file for printing, archival or further analysis.

Reference: Oberto, J. Bioinformatics (2007); doi: 10.1093/bioinformatics/btm600
[Abstract] [PDF article]

ArchaeaXML is a web service that seamlessly integrates a PubMed RSS feed into a dynamic web page. It parses the XML response of the RSS feed and sends the updated results directly to the web browser. The RSS contents are updated on a daily basis by PubMed. This customized RSS feed responds to the query string: "archae* NOT archaeol* NOT archaean".

This software is mainly a proof of concept for a minimalistic web application and is currently under development