Databases of homologous gene families for comparative genomics (2009)
Penel, Simon, Arigon, Anne-Muriel, Dufayard, Jean-François, Sertier, Anne-Sophie, Daubin, Vincent, Duret, Laurent, ...
Abstract Background Comparative genomics is a central step in many sequence analysis studies, from gene annotation and the identification of new functional regions in genomes, to the study of...
Databases of Homologous Gene Families for Comparative Genomics (2009)
Penel, Simon, Arigon, Anne-Muriel, Dufayard, Jean-François, Sertier, Anne-Sophie, Daubin, Vincent, Duret, Laurent, ...
Background: Comparative genomics is a central step in many sequence analysis studies, from gene annotation and the identification of new functional regions in genomes, to the study of evolutionary...
Databases of Homologous Gene Families for Comparative Genomics (2009)
Penel, Simon, Arigon, Anne-Muriel, Dufayard, Jean-François, Sertier, Anne-Sophie, Daubin, Vincent, Duret, Laurent, ...
Background: Comparative genomics is a central step in many sequence analysis studies, from gene annotation and the identification of new functional regions in genomes, to the study of evolutionary...
Second release of HOGENOM, a database of homologous genes from (2008)
Simon Penel, Pascal Calvat, Jean-françois Dufayard, Laurent Duret, Manolo Gouy, Guy Perrière
complete genomes
Data Retrieval and Handling Tools for the PBIL Gene Family Databases (2008)
Guy Perrière, Jean-françois Dufayard, Simon Penel, Julien Grassot, Laurent Duret, Manolo Gouy, ...
Different homologous gene family databases have been developed and are maintained at the PBIL (Pôle Bioinformatique Lyonnais). Historically, the first one was HOVERGEN, a collection of homologous...
Bioinformatic sequence identification from sequence family (2008)
Anne-muriel Arigon, Guy Perrière, Manolo Gouy
databases
BIOINFORMATICS ORIGINAL PAPER Sequence analysis (2008)
Jean-françois Dufayard, Laurent Duret, Simon Penel, Manolo Gouy, François Rechenmann, Guy Perrière
doi:10.1093/bioinformatics/bti325 Tree pattern matching in phylogenetic trees: automatic search for orthologs or paralogs in homologous gene sequence databases
Ian B. Jeffery, Stephen F. Madden, Paul A. Mcgettigan, Guy Perrière, Aedín C. Culhane, Desmond G. Higgins, ...
transcription factor binding site information with gene
A universal feature in Bacteria (2008)
G+c V. Jobim, Daubin G. Perrière, Vincent Daubin, Guy Perrière
along the genome: A universal feature in Bacteria G+C3 structuring along the genome:
The non-redundant Baci lus subtilis (NRSub) database: update 1998 (2007)
Guy Perrière, Manolo Gouy, Takashi Gojobori
The non-redundant Bacillus subtilis database (NRSub) has been developed in the context of the sequencing project devoted to this bacterium. As this project has reached completion, the whole genome is...
HOBACGEN: Database System (2007)
For Comparative Genomics, Guy Perrière, Laurent Duret, Manolo Gouy
this article were defrayed in part by payment of page charges. This article must therefore be hereby marked "advertisement" in accordance with 18 USC section 1734 solely to indicate this...
Integrating transcription factor binding site information with gene expression datasets (2007)
Jeffery, Ian B., Madden, Stephen F., McGettigan, Paul A., Perrière, Guy, Culhane, Aedín C., Higgins, Desmond G.
Motivation: Microarrays are widely used to measure gene expression differences between sets of biological samples. Many of these differences will be due to differences in the activities of...
Origin and Molecular Evolution of Receptor Tyrosine Kinases with Immunoglobulin-Like Domains (2006)
Grassot, Julien, Gouy, Manolo, Perrière, Guy, Mouchiroud, Guy
Receptor tyrosine kinases (RTKs) are involved in the control of fundamental cellular processes in metazoans. In vertebrates, RTK could be grouped in distinct classes based on the nature of their...
Origin and Molecular Evolution of Receptor Tyrosine Kinases with Immunoglobulin-like Domains (2006)
Grassot, Julien, Gouy, Manolo, Perrière, Guy, Mouchiroud, Guy
Receptor tyrosine kinases (RTK) are involved in the control of fundamental cellular processes in metazoans. In vertebrates, RTK could be grouped in distinct classes based on the nature of their...
HoSeqI: automated homologous sequence identification in gene family databases (2006)
Arigon, Anne-Muriel, Perrière, Guy, Gouy, Manolo
Summary: We present a web service allowing to automatically assign sequences to homologous gene families from a set of databases. After identification of the most similar gene family to the query...
Baty, Florent, Bihl, Michel P, Perrière, Guy, Culhane, Aedín C, Brutsche, Martin H
Abstract Background A recent publication described a supervised classification method for microarray data: Between Group Analysis (BGA). This method which is based on performing multivariate...
BIOINFORMATICS APPLICATIONS NOTE (2005)
Gene Expression, Aedín C. Culhane, Jean Thioulouse, Guy Perrière, Desmond G. Higgins
MADE4: an R package for multivariate analysis of gene expression data Vol. 21 no. 11 2005, pages 2789–2790 doi:10.1093/bioinformatics/bti394
Dufayard, Jean-François, Duret, Laurent, Penel, Simon, Gouy, Manolo, Rechenmann, François, Perrière, Guy
Motivation: Comparative sequence analysis is widely used to study genome function and evolution. This approach first requires the identification of homologous genes and then the interpretation of...
MADE4: an R package for multivariate analysis of gene expression data (2005)
Culhane, Aedín C., Thioulouse, Jean, Perrière, Guy, Higgins, Desmond G.
Summary: MADE4, microarray ade4, is a software package that facilitates multivariate analysis of microarray gene-expression data. MADE4 accepts a wide variety of gene-expression data formats. MADE4...
Dufayard, Jean-François, Duret, Laurent, Penel, Simon, Gouy, Manolo, Rechenmann, François, Perrière, Guy
Motivation: Comparative sequence analysis is widely used to study genome function and evolution. This approach first requires the identification of homologous genes and then the interpretation of...
MADE4: an R package for multivariate analysis of gene expression data (2005)
Culhane, Aedín C., Thioulouse, Jean, Perrière, Guy, Higgins, Desmond G.
Summary: MADE4, microarray ade4, is a software package that facilitates multivariate analysis of microarray gene expression data. MADE4 accepts a wide variety of gene expression data formats. MADE4...
The European ribosomal RNA database (2004)
Wuyts, Jan, Perrière, Guy, Van De Peer, Yves
The European ribosomal RNA database aims to compile all complete or nearly complete ribosomal RNA sequences from both the small (SSU) and large (LSU) ribosomal subunits. All sequences are available...
Update of NUREBASE: nuclear hormone receptor functional genomics (2004)
Ruau, David, Duarte, Jorge, Ourjdal, Tarik, Perrière, Guy, Laudet, Vincent, Robinson-Rechavi, Marc
Nuclear hormone receptors are an abundant class of ligand‐activated transcriptional regulators, found in varying numbers in all animals. Based on our experience of managing the official...
Cross-platform comparison and visualisation of gene expression data using co-inertia analysis (2003)
Culhane, Aedín C, Perrière, Guy, Higgins, Desmond G
Abstract Background Rapid development of DNA microarray technology has resulted in different laboratories adopting numerous different protocols and technological platforms, which has severely...
The source of laterally transferred genes in bacterial genomes (2003)
Daubin, Vincent, Lerat, Emmanuelle, Perrière, Guy
Abstract Background Laterally transferred genes have often been identified on the basis of compositional features that distinguish them from ancestral genes in the genome. These genes are usually...
RTKdb: database of receptor tyrosine kinase (2003)
Julien Grassot, Guy Mouchiroud, Guy Perrière
Receptor Tyrosine Kinases (RTK) are transmembrane receptors specifically found in metazoans. They represent an excellent model for studying evolution of cellular processes in metazoans because they...
Integrated databanks access and sequence/structure analysis services at the PBIL (2003)
Guy Perrière, Christophe Combet, Simon Penel, Christophe Blanchet, Jean Thioulouse, ...
The World Wide Web server of the PBIL (Po le Bioinformatique Lyonnais) provides on-line access to sequence databank and to many tools of nucleic acid and protein sequence analyses. This server allows...
G+C3 Structuring Along the Genome: A Common Feature in Prokaryotes (2003)
Daubin, Vincent, Perrière, Guy
The heterogeneity of gene nucleotide content in prokaryotic genomes is commonly interpreted as the result of three main phenomena: (1) genes undergo different selection pressures both during and...
G+C3 Structuring along the Genome: A Common Feature in Prokaryotes (2003)
Daubin, Vincent, Perrière, Guy
The heterogeneity of gene nucleotide content in prokaryotic genomes is commonly interpreted as the result of three main phenomena: i) genes undergo different selection pressures both during and after...
Integrated databanks access and sequence/structure analysis services at the PBIL (2003)
Perrière, Guy, Combet, Christophe, Penel, Simon, Blanchet, Christophe, Thioulouse, Jean, Geourjon, Christophe, ...
The World Wide Web server of the PBIL (Pôle Bioinformatique Lyonnais) provides on-line access to sequence databanks and to many tools of nucleic acid and protein sequence analyses. This server...
RTKdb: database of receptor tyrosine kinase (2003)
Grassot, Julien, Mouchiroud, Guy, Perrière, Guy
Receptor Tyrosine Kinases (RTK) are transmembrane receptors specifically found in metazoans. They represent an excellent model for studying evolution of cellular processes in metazoans because they...
G+C3 Structuring along the Genome: A Common Feature in Prokaryotes (2003)
Daubin, Vincent, Perrière, Guy
The heterogeneity of gene nucleotide content in prokaryotic genomes is commonly interpreted as the result of three main phenomena: i) genes undergo different selection pressures both during and after...
NUREBASE: database of nuclear hormone receptors (2002)
Duarte, Jorge, Perrière, Guy, Laudet, Vincent, Robinson-Rechavi, Marc
Nuclear hormone receptors are an abundant class of ligand activated transcriptional regulators, found in varying numbers in all animals. Based on our experience of managing the official nomenclature...
Between-group analysis of microarray data (2002)
Culhane, Aedín C., Perrière, Guy, Considine, Elizabeth C., Cotter, Thomas G., Higgins, Desmond G.
Motivation: Most supervised classification methods are limited by the requirement for more cases than variables. In microarray data the number of variables (genes) far exceeds the number of cases...
Use and misuse of correspondence analysis in codon usage studies (2002)
Perrière, Guy, Thioulouse, Jean
Correspondence analysis has frequently been used for codon usage studies but this method is often misused. Because amino acid composition exerts constraints on codon usage, it is common to use tables...
EMGLib: the Enhanced Microbial Genomes Library (update 2000) (2000)
Perrière, Guy, Bessières, Philippe, Labedan, Bernard
As the number of complete microbial genomes publicly available is still growing, the problem of annotation quality in these very large sequences remains unsolved. Indeed, the number of annotations...
The Enhanced Microbial Genomes Library (1999)
Guy Perrière, Philippe Bessières, Bernard Labedan
Since the obtention of the complete sequence of Haemophilus influenzae Rd in 1995, the number of bacterial genomes entirely sequenced has regularly increased. A problem is that the quality of the...
The non-redundant Bacillus subtilis (NRSub) database: update 1998 (1998)
Guy Perrière, Manolo Gouy, Takashi Gojobori
The non-redundant Bacillus subtilis database (NRSub) has been developed in the context of the sequencing project devoted to this bacterium. As this project has reached completion, the whole genome is...
The NRSub database: update 1997 (1997)
Guy Perrière, Ivan Moszer, Takashi Gojobori
In the context of the international project aiming at sequencing the whole genome of Bacillus subtilis we have developed NRSub, a non-redundant database of sequences from this organism. Starting from...
On-line tools for sequence retrieval and multivariate statistics in molecular biology (1996)
Perrière, Guy, Thioulouse, Jean
We have developed a World-Wide Web server for browsing sequence collections structured under the ACNUC format and for performing multivariate analyses on sequences. General collections (like GenBank...
NRSub: a non-redundant database for Bacillus subtilis (1995)
Guy Perrière, Ivan Moszer, Takashi Gojobori
In the context of the international project aimed at sequencing the whole genome of Bacillus subtilis we have developed a non-redundant, fully annotated database of sequences from this organism....
NUREBASE: database of nuclear hormone receptors
Duarte, Jorge, Perrière, Guy, Laudet, Vincent, Robinson-Rechavi, Marc
Nuclear hormone receptors are an abundant class of ligand activated transcriptional regulators, found in varying numbers in all animals. Based on our experience of managing the official nomenclature...
EMGLib: the Enhanced Microbial Genomes Library (update 2000)
Perrière, Guy, Bessières, Philippe, Labedan, Bernard
As the number of complete microbial genomes publicly available is still growing, the problem of annotation quality in these very large sequences remains unsolved. Indeed, the number of annotations...
Use and misuse of correspondence analysis in codon usage studies
Perrière, Guy, Thioulouse, Jean
Correspondence analysis has frequently been used for codon usage studies but this method is often misused. Because amino acid composition exerts constraints on codon usage, it is common to use tables...
RTKdb: database of receptor tyrosine kinase
Grassot, Julien, Mouchiroud, Guy, Perrière, Guy
Receptor Tyrosine Kinases (RTK) are transmembrane receptors specifically found in metazoans. They represent an excellent model for studying evolution of cellular processes in metazoans because they...
Integrated databanks access and sequence/structure analysis services at the PBIL
Perrière, Guy, Combet, Christophe, Penel, Simon, Blanchet, Christophe, Thioulouse, Jean, Geourjon, Christophe, ...
The World Wide Web server of the PBIL (Pôle Bioinformatique Lyonnais) provides on-line access to sequence databanks and to many tools of nucleic acid and protein sequence analyses. This server...
A Phylogenomic Approach to Bacterial Phylogeny: Evidence of a Core of Genes Sharing a Common History
Daubin, Vincent, Gouy, Manolo, Perrière, Guy
It has been claimed that complete genome sequences would clarify phylogenetic relationships between organisms, but up to now, no satisfying approach has been proposed to use efficiently these data....
The source of laterally transferred genes in bacterial genomes
Daubin, Vincent, Lerat, Emmanuelle, Perrière, Guy
Contrary to previous hypotheses that methods for identifying laterally transferred genes cannot detect genes with similar base composition to that of the donor organism, it is suggested that the...
Update of NUREBASE: nuclear hormone receptor functional genomics
Ruau, David, Duarte, Jorge, Ourjdal, Tarik, Perrière, Guy, Laudet, Vincent, Robinson-Rechavi, Marc
Nuclear hormone receptors are an abundant class of ligand-activated transcriptional regulators, found in varying numbers in all animals. Based on our experience of managing the official nomenclature...
The European ribosomal RNA database
Wuyts, Jan, Perrière, Guy, Van De Peer, Yves
The European ribosomal RNA database aims to compile all complete or nearly complete ribosomal RNA sequences from both the small (SSU) and large (LSU) ribosomal subunits. All sequences are available...
HOBACGEN: Database System for Comparative Genomics in Bacteria
Perrière, Guy, Duret, Laurent, Gouy, Manolo
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 from SWISS-PROT/TrEMBL...
Ginolhac, Aurélien, Jarrin, Cyrille, Gillet, Benjamin, Robe, Patrick, Pujic, Petar, Tuphile, Karine, ...
The metagenomic approach provides direct access to diverse unexplored genomes, especially from uncultivated bacteria in a given environment. This diversity can conceal many new biosynthetic pathways....
NUREBASE: database of nuclear hormone receptors
Duarte, Jorge, Perrière, Guy, Laudet, Vincent, Robinson-Rechavi, Marc
Nuclear hormone receptors are an abundant class of ligand activated transcriptional regulators, found in varying numbers in all animals. Based on our experience of managing the official nomenclature...
EMGLib: the Enhanced Microbial Genomes Library (update 2000)
Perrière, Guy, Bessières, Philippe, Labedan, Bernard
As the number of complete microbial genomes publicly available is still growing, the problem of annotation quality in these very large sequences remains unsolved. Indeed, the number of annotations...
Use and misuse of correspondence analysis in codon usage studies
Perrière, Guy, Thioulouse, Jean
Correspondence analysis has frequently been used for codon usage studies but this method is often misused. Because amino acid composition exerts constraints on codon usage, it is common to use tables...
RTKdb: database of receptor tyrosine kinase
Grassot, Julien, Mouchiroud, Guy, Perrière, Guy
Receptor Tyrosine Kinases (RTK) are transmembrane receptors specifically found in metazoans. They represent an excellent model for studying evolution of cellular processes in metazoans because they...
Integrated databanks access and sequence/structure analysis services at the PBIL
Perrière, Guy, Combet, Christophe, Penel, Simon, Blanchet, Christophe, Thioulouse, Jean, Geourjon, Christophe, ...
The World Wide Web server of the PBIL (Pôle Bioinformatique Lyonnais) provides on-line access to sequence databanks and to many tools of nucleic acid and protein sequence analyses. This server...
A Phylogenomic Approach to Bacterial Phylogeny: Evidence of a Core of Genes Sharing a Common History
Daubin, Vincent, Gouy, Manolo, Perrière, Guy
It has been claimed that complete genome sequences would clarify phylogenetic relationships between organisms, but up to now, no satisfying approach has been proposed to use efficiently these data....
The source of laterally transferred genes in bacterial genomes
Daubin, Vincent, Lerat, Emmanuelle, Perrière, Guy
Contrary to previous hypotheses that methods for identifying laterally transferred genes cannot detect genes with similar base composition to that of the donor organism, it is suggested that the...
Update of NUREBASE: nuclear hormone receptor functional genomics
Ruau, David, Duarte, Jorge, Ourjdal, Tarik, Perrière, Guy, Laudet, Vincent, Robinson-Rechavi, Marc
Nuclear hormone receptors are an abundant class of ligand-activated transcriptional regulators, found in varying numbers in all animals. Based on our experience of managing the official nomenclature...
The European ribosomal RNA database
Wuyts, Jan, Perrière, Guy, Van De Peer, Yves
The European ribosomal RNA database aims to compile all complete or nearly complete ribosomal RNA sequences from both the small (SSU) and large (LSU) ribosomal subunits. All sequences are available...
HOBACGEN: Database System for Comparative Genomics in Bacteria
Perrière, Guy, Duret, Laurent, Gouy, Manolo
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 from SWISS-PROT/TrEMBL...
Ginolhac, Aurélien, Jarrin, Cyrille, Gillet, Benjamin, Robe, Patrick, Pujic, Petar, Tuphile, Karine, ...
The metagenomic approach provides direct access to diverse unexplored genomes, especially from uncultivated bacteria in a given environment. This diversity can conceal many new biosynthetic pathways....
Horizontal Gene Transfer Regulation in Bacteria as a “Spandrel” of DNA Repair Mechanisms
Fall, Saliou, Mercier, Anne, Bertolla, Franck, Calteau, Alexandra, Gueguen, Laurent, Perrière, Guy, ...
Horizontal gene transfer (HGT) is recognized as the major force for bacterial genome evolution. Yet, numerous questions remain about the transferred genes, their function, quantity and frequency. The...