The Generation Challenge Programme comparative plant stress-responsive gene catalogue

The Generation Challenge Programme (GCP; www.generationcp.org) has developed an online resource documenting stress-responsive genes comparatively across plant species. This public resource is a compendium of protein families, phylogenetic trees, multiple sequence alignments (MSA) and associated experimental evidence. The central objective of this resource is to elucidate orthologous and paralogous relationships between plant genes that may be involved in response to environmental stress, mainly abiotic stresses such as water deficit (‘drought’). The web-based graphical user interface (GUI) of the resource includes query and visualization tools that allow diverse searches and browsing of the underlying project database. The web interface can be accessed at http://dayhoff.generationcp.org.

[1]  E. Koonin.  Orthologs, Paralogs, and Evolutionary Genomics 1 , 2005 .

[2]  Cornelia I Bargmann,et al.  Comparing genomic expression patterns across species identifies shared transcriptional profile in aging , 2004, Nature Genetics.

[3]  Sean R. Eddy,et al.  ATV: display and manipulation of annotated phylogenetic , 2001, Bioinform..

[4]  Heiko Schoof,et al.  BioMOBY Successfully Integrates Distributed Heterogeneous Bioinformatics Web Services. The PlaNet Exemplar Case1 , 2005, Plant Physiology.

[5]  K. Sjölander,et al.  FlowerPower: clustering proteins into domain architecture classes for phylogenomic inference of protein function , 2007, BMC evolutionary biology.

[6]  Duncan P. Brown,et al.  Functional Classification Using Phylogenomic Inference , 2006, PLoS Comput. Biol..

[7]  E. Koonin.  Orthologs, paralogs, and evolutionary genomics. , 2005, Annual review of genetics.

[8]  Thomas L. Madden,et al.  BLAST: at the core of a powerful and diverse set of sequence analysis tools , 2004, Nucleic Acids Res..

[9]  R. DeSalle,et al.  Gene family evolution and homology: genomics meets phylogenetics. , 2000, Annual review of genomics and human genetics.

[10]  Kimmen Sjölander,et al.  Berkeley Phylogenomics Group web servers: resources for structural phylogenomic analysis , 2007, Nucleic Acids Res..

[11]  Chris Mungall,et al.  A Chado case study: an ontology-based modular schema for representing genome-associated biological information , 2007, ISMB/ECCB.

[12]  Robert C. Edgar,et al.  MUSCLE: multiple sequence alignment with high accuracy and high throughput. , 2004, Nucleic acids research.

[13]  Geoffrey J. Barton,et al.  The Jalview Java alignment editor , 2004, Bioinform..

[14]  S. Bergmann,et al.  Similarities and Differences in Genome-Wide Expression Data of Six Organisms , 2003, PLoS biology.

[15]  G. Gibson,et al.  Cross-species comparison of genome-wide expression patterns , 2004, Genome Biology.

[16]  M F Lawrence,et al.  Impedance-based detection of DNA sequences using a silicon transducer with PNA as the probe layer. , 2004, Nucleic acids research.

[17]  Kimmen Sjölander,et al.  Phylogenomic inference of protein molecular function: advances and challenges , 2004, Bioinform..