Summary: MADE4, microarray ade4, is a software package that facilitates multivariate analysis of gene-expression data. MADE4 accepts wide variety data formats. takes advantage the extensive statistical and graphical functions in R extending these for application to In addition, provides new visualization tools aid interpretation

Abstract Motivation: Most supervised classification methods are limited by the requirement for more cases than variables. In microarray data number of variables (genes) far exceeds (arrays), and thus filtering pre-selection genes is required. We describe application Between Group Analysis (BGA) to analysis data. A feature BGA that it can be used when (arrays). based on carrying out an ordination groups samples, using a standard method such as Correspondence (COA), rather individual samples....

Motivation: Comparative sequence analysis is widely used to study genome function and evolution. This approach first requires the identification of homologous genes then interpretation their homology relationships (orthology or paralogy). To provide help in this complex task, we developed three databases containing sequences, multiple alignments phylogenetic trees: HOBACGEN, HOVERGEN HOGENOM. In paper, present two new tools for automating search orthologs paralogs these databases.

Abstract Background Comparative genomics is a central step in many sequence analysis studies, from gene annotation and the identification of new functional regions genomes, to study evolutionary processes at molecular level (speciation, single or whole genome duplications, etc.) phylogenetics. In that context, databases providing users high quality homologous families alignments as well phylogenetic trees based on state art algorithms are becoming indispensable. Methods We developed an...

Laterally transferred genes have often been identified on the basis of compositional features that distinguish them from ancestral in genome. These are usually A+T-rich, arguing either there is a bias towards acquiring donor organisms having low G+C contents or acquired similar genomic base compositions go undetected these analyses.By examining genome closely related, fully sequenced bacteria, we uncovered confined to single and examined sequence genes. The analysis shows few transfer events...

ABSTRACT BIBI was designed to automate DNA sequence analysis for bacterial identification in the clinical field. relies on use of BLAST and CLUSTAL W programs applied different subsets sequences extracted from GenBank. These are filtered stored a new database, which is adapted identification.

Correspondence analysis has frequently been used for codon usage studies but this method is often misused. Because amino acid composition exerts constraints on usage, it common to use tables containing relative frequencies (or ratios of frequencies) instead simple counts get rid these biases. The problem that some important properties correspondence analysis, such as rows weighting, are lost in the process. Moreover, measures sometimes introduces other biases and diminishes quantity...

Rapid development of DNA microarray technology has resulted in different laboratories adopting numerous protocols and technological platforms, which severely impacted on the comparability array data. Current cross-platform comparison gene expression data are usually based cross-referencing annotation each transcript represented arrays, extracting a list genes common to all arrays comparing this subset. Unfortunately, filtering subset across often excludes many thousands genes, because...

Correspondence analysis of codon usage data is a widely used method in sequence analysis, but the variability amino acid composition between proteins confounding factor when one wants to analyse synonymous variability. A simple and natural way cope with this problem use within-group correspondence analysis. There is, however, no user-friendly implementation available for genomic studies. Our motivation was provide community Web facility easily study on subset public databases.Availability...

Horizontal gene transfer (HGT) is recognized as the major force for bacterial genome evolution. Yet, numerous questions remain about transferred genes, their function, quantity and frequency. The extent to which genetic transformation by exogenous DNA has occurred over evolutionary time was initially addressed an in silico approach using complete sequence of Ralstonia solanacearum GMI1000 strain. Methods based on phylogenetic reconstruction prokaryote homologous genes families detected 151...

Estimating the phylogenetic position of bacterial and archaeal organisms by genetic sequence comparisons is considered as gold-standard in taxonomy. This also a way to identify species origin sequence. The quality reference database used such analyses crucial: must reflect up-to-date nomenclature accurately indicate its sequences.

We present here HOBACGEN, a database system devoted to comparative genomics in bacteria. HOBACGEN contains all available protein genes from bacteria, archaea, and yeast, taken SWISS-PROT/TrEMBL classified into families. It also includes multiple alignments phylogenetic trees built these The is organized under client/server architecture with client written Java, which may run on any platform. This integrates graphical interface allowing users select families according various criteria notably...

Receptor tyrosine kinases (RTKs) are involved in the control of fundamental cellular processes metazoans. In vertebrates, RTK could be grouped distinct classes based on nature their cognate ligand and modular composition extracellular domain. with immunoglobulin-like domains (IG-like RTK) encompass several have been found early metazoans, including sponges. Evolution IG-like is characterized by extended molecular functional diversification, which prompted us to study evolutionary history....

Summary Ecological and evolutionary processes involved in magnetotactic bacteria (MTB) adaptation to their environment have been a matter of debate for many years. Ongoing efforts characterization are progressively contributing understand these processes, including the genetic molecular mechanisms responsible biomineralization. Despite numerous culture‐independent MTB characterizations, essentially within Proteobacteria phylum, only few species isolated culture because complex growth...

Terpenes represent one of the largest and most diversified families natural compounds are used in numerous industrial applications. Terpene synthase (TPS) genes originated bacteria as diterpene (di-TPS) genes. They also found plant fungal genomes. The recent availability a large number genomes represents an opportunity to investigate how involved synthesis were acquired by fungi, assess consequences this process on metabolism. In order origin di-TPS, we implemented search for potential...

Receptor Tyrosine Kinases (RTK) are transmembrane receptors specifically found in metazoans. They represent an excellent model for studying evolution of cellular processes metazoans because they encompass large families modular proteins and belong to a major family contingency generating molecules eukaryotic cells: the protein kinases. Because tyrosine kinases have been under close scrutiny many years various species, associated with wealth information, mainly mammals. Presently, most...

This report describes two applications of a multivariate method for studying classes nucleotide or protein sequences: correspondence discriminant analysis (CDA). The first example is the discrimination between Escherichia coli proteins according to their subcellular location (membrane, cytoplasm and periplasm). high resolution made it possible predict E.coli whom this information not known. second coding sequences leading lagging strands in four bacteria: Mycoplasma genitalium, Haemophilus...

Abstract Background Phosphatidylinositol-3-kinases (PI3Ks) are a family of eukaryotic enzymes modifying phosphoinositides in phosphatidylinositols-3-phosphate. Located upstream the AKT/mTOR signalling pathway, PI3Ks activate secondary messengers extracellular signals. They involved many critical cellular processes such as cell survival, angiogenesis and autophagy. PI3K is divided into three classes, including 14 human homologs. While class II composed single catalytic subunit, I III also...