SyntTax: Prokaryotic Synteny and Taxonomy Explorer
The study of the conservation of gene order or synteny constitutes a powerful
methodology to assess the orthology of genomic regions and to predict functional
relationships between genes. The exponential growth of microbial genomic databases
is expected to improve synteny predictions significantly. Paradoxically, this
genomic data plethora, without information on organisms relatedness, could
impair the performance of synteny analysis programs.
In this work, I present SyntTax, a synteny web service designed to take full
advantage of the large amount or archaeal and bacterial genomes by linking them
through taxonomic relationships. SyntTax incorporates a full hierarchical
taxonomic tree allowing intuitive access to all completely sequenced prokaryotes.
Single or multiple organisms can be chosen on the basis of their lineage by
selecting the corresponding rank nodes in the tree. The synteny methodology is
built upon our previously described Absynte algorithm with several additional
SyntTax aims to produce robust syntenies by providing prompt access to the
taxonomic relationships connecting all completely sequenced microbial genomes.
The reduction in redundancy offered by lineage selection presents the benefit
of increasing accuracy while reducing computation time. This web tool was used
to resolve successfully several conserved complex gene clusters described in
the literature. In addition, particular features of SyntTax permit the
confirmation of the involvement of the four components constituting the E.
coli YgjD multiprotein complex responsible for tRNA modification. By analyzing
the clustering evolution of alternative gene fusions, new proteins potentially
interacting with this complex could be proposed.
Absynte: Archaeal and Bacterial SYNTeny Explorer
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: Fast Investigation Tool for Archaeal
& Bacterial Regulons
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: Bacterial and Archaeal Gene Exploration Tool
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: Latest bibliography on archaea
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".
REVCOMP: Reverse Complement a DNA sequence
This software is mainly a proof of concept for a minimalistic web
application and is currently under development