Biomedical subjects

Laurent Bianchetti

Publications and source records attributed to Laurent Bianchetti.

4 recordsLinked to original sources

PubMed2006

PromAn: an integrated knowledge-based web server dedicated to promoter analysis.

PromAn is a modular web-based tool dedicated to promoter analysis that integrates distinct complementary databases, methods and programs. PromAn provides automatic analysis of a genomic region with minimal prior knowledge of the genomic sequence. Prediction programs and experimental databases are combined to locate the transcription start site (TSS) and the promoter region within a large genomic input sequence. Transcription factor binding sites (TFBSs) can be predicted using several public databases and user-defined motifs. Also, a phylogenetic footprinting strategy, combining multiple alignment of large genomic sequences and assignment of various scores reflecting the evolutionary selection pressure, allows for evaluation and ranking of TFBS predictions. PromAn results can be displayed in an interactive graphical user interface, PromAnGUI. It integrates all of this information to highlight active promoter regions, to identify among the huge number of TFBS predictions those which are the most likely to be potentially functional and to facilitate user refined analysis. Such an integrative approach is essential in the face of a growing number of tools dedicated to promoter analysis in order to propose hypotheses to direct further experimental validations. PromAn is publicly available at http://bips.u-strasbg.fr/PromAn.

Binding Sites↗

PubMed2005

vALId: validation of protein sequence quality based on multiple alignment data.

The validation of sequences is essential to perform accurate phylogeny and structure/function analysis. However among the thousands of protein sequences available in the public databases, most have been predicted in silico and have not systematically undergone a quality verification. It has recently become evident that they often contain sequence errors. To address the problem of automatic protein quality control, we have developed vALId, an interactive web interfaced software. Taking advantage of high quality multiple alignments of complete protein sequences (MACS), vALId first warns about the presence of suspicious insertions, deletions (indels) and divergent segments, and second, proposes corrections based on transcripts and genome contigs. In a first evaluation test, hundreds of indels and divergent segments were randomly generated in a manually refined MACS. The sensitivity (Sn) and specificity (Sp) of indel detection were excellent (0.96) while the mean Sn(0.49) and Sp(0.56) of divergent segment delineation depended on the percent identity between sequence neighbors. In a second test, 6195 sequences in 100 MACS corresponding to different functional and structural protein families were analyzed. 65% of the sequences were in silico predictions and 44% of eukaryote predicted proteins were partially incorrect with at least one suspicious indel or divergent segment.

Algorithms↗

PubMed2003

PipeAlign: A new toolkit for protein family analysis.

PipeAlign is a protein family analysis tool integrating a five step process ranging from the search for sequence homologues in protein and 3D structure databases to the definition of the hierarchical relationships within and between subfamilies. The complete, automatic pipeline takes a single sequence or a set of sequences as input and constructs a high-quality, validated MACS (multiple alignment of complete sequences) in which sequences are clustered into potential functional subgroups. For the more experienced user, the PipeAlign server also provides numerous options to run only a part of the analysis, with the possibility to modify the default parameters of each software module. For example, the user can choose to enter an existing multiple sequence alignment for refinement, validation and subsequent clustering of the sequences. The aim is to provide an interactive workbench for the validation, integration and presentation of a protein family, not only at the sequence level, but also at the structural and functional levels. PipeAlign is available at http://igbmc.u-strasbg.fr/PipeAlign/.

Internet↗

PubMed2002

M13 endopeptidases: New conserved motifs correlated with structure, and simultaneous phylogenetic occurrence of PHEX and the bony fish.

M13 endopeptidase alignments have focused mainly on mammalian sequences and on the active site region defining the catalytic sequence signatures. Aligning all available M13 from bacteria to human on a full-length basis, we have performed a sequence analysis. This enabled us to highlight the origin and function of the M13 PHEX subtype family endopeptidase (phosphate regulating gene with homologies to endopeptidases on the X chromosome). New evolutionary conserved regions in both prokaryotes and eukaryotes have been detected and eukaryotic-specific regions clearly delineated. Using the recently solved neprilysin structure, we have observed that all new motifs, except one, localize in the spatial vicinity of the previously reported catalytic signatures. Interestingly, a highly hydrophobic pocket containing three newly reported motifs is centered by the C-terminal tryptophan residue. Extensive M13 searches in complete and in progress higher eukaryotic genomes have lead to the identification of Danio rerio as the simplest organism having PHEX. Finally, the human PHEX substrate, the parathyroid hormone-related peptide, PTHrP(107-139), is absent in bony fish: this suggests the existence of further PHEX substrates common to both bony fishes and higher vertebrates.

Amino Acid Motifs↗