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PHYTOPROT: a database of clusters of plant proteins

S. Mohseni-Zadeh
2004 Nucleic Acids Research  
All the protein sequences from plants (including Arabidopsis thaliana) available from SwissProt/ TrEMBL have been the subject of an all-by-all systematic comparison and grouped into clusters of related  ...  The user can also launch a BLAST search of a query sequence against all the clusters.  ...  Pereira and Ge Ânoplante-Info for their help in setting up the Oracle database, to Infobiogen for help in using its multi-threaded machine and to J. Gouzy for his generous gift of the XDOM program.  ... 
doi:10.1093/nar/gkh040 pmid:14681432 pmcid:PMC308774 fatcat:az5ze23rkfhltcog3lrl4jukhi

Massive Sequence Comparisons as a Help in Annotating Genomic Sequences

A. Louis
2001 Genome Research  
The publication costs of this article were defrayed in part by payment of page charges.  ...  Although the PHYTOPROT database should prove useful for the annotation of plant genomes-particularly that of A. thaliana-the present release is outdated and needs an update.  ...  An all-by-all comparison of all the publicly available protein sequences from plants has been performed, followed by a clusterization process.  ... 
doi:10.1101/gr.gr-1776r pmid:11435413 pmcid:PMC311131 fatcat:mcjgqs7ftfg7pcr5rpcwbvddzu

The Molecular Biology Database Collection: 2008 update

Michael Y. Galperin
2007 Nucleic Acids Research  
The growing number of databases related to immunology, plant and organelle research have been accommodated by separating them into three new categories.  ...  The databases are organized in a hierarchical classification that simplifies the process of finding the right database for any given task.  ...  Continued Clusters of (predicted) plant proteins http://genoplante-info.infobiogen.fr/phytoprot PlantsP/PlantsT Plant proteins involved in phosphorylation and transport http://plantsp.sdsc.edu/ 588 TIGR  ... 
doi:10.1093/nar/gkm1037 pmid:18025043 pmcid:PMC2238887 fatcat:y5pnrvfxmjfspnllaykn5pohoq

The Molecular Biology Database Collection: 2006 update

M. Y. Galperin
2006 Nucleic Acids Research  
The growing number of databases related to immunology, plant and organelle research have been accommodated by separating them into three new categories.  ...  The databases are organized in a hierarchical classification that simplifies the process of finding the right database for any given task.  ...  Continued Clusters of (predicted) plant proteins http://genoplante-info.infobiogen.fr/phytoprot PlantsP/PlantsT Plant proteins involved in phosphorylation and transport http://plantsp.sdsc.edu/ 588 TIGR  ... 
doi:10.1093/nar/gkj162 pmid:16381871 pmcid:PMC1347524 fatcat:rf33e65pcjatbjiqpnloykyvne

The Molecular Biology Database Collection: 2004 update

M. Y. Galperin
2004 Nucleic Acids Research  
The growing number of databases related to immunology, plant and organelle research have been accommodated by separating them into three new categories.  ...  The databases are organized in a hierarchical classification that simplifies the process of finding the right database for any given task.  ...  Continued Clusters of (predicted) plant proteins http://genoplante-info.infobiogen.fr/phytoprot PlantsP/PlantsT Plant proteins involved in phosphorylation and transport http://plantsp.sdsc.edu/ 588 TIGR  ... 
doi:10.1093/nar/gkh143 pmid:14681349 pmcid:PMC308877 fatcat:sfmdf43aezccfjmcmrbsilsh7m

The Molecular Biology Database Collection: 2007 update

M. Y. Galperin
2007 Nucleic Acids Research  
The growing number of databases related to immunology, plant and organelle research have been accommodated by separating them into three new categories.  ...  The databases are organized in a hierarchical classification that simplifies the process of finding the right database for any given task.  ...  Continued Clusters of (predicted) plant proteins http://genoplante-info.infobiogen.fr/phytoprot PlantsP/PlantsT Plant proteins involved in phosphorylation and transport http://plantsp.sdsc.edu/ 588 TIGR  ... 
doi:10.1093/nar/gkl1008 pmid:17148484 pmcid:PMC1761423 fatcat:auqafva4mnfhzoz67cpq2qtwyq

The Molecular Biology Database Collection: 2005 update

M. Y. Galperin
2004 Nucleic Acids Research  
The growing number of databases related to immunology, plant and organelle research have been accommodated by separating them into three new categories.  ...  The databases are organized in a hierarchical classification that simplifies the process of finding the right database for any given task.  ...  Continued Clusters of (predicted) plant proteins http://genoplante-info.infobiogen.fr/phytoprot PlantsP/PlantsT Plant proteins involved in phosphorylation and transport http://plantsp.sdsc.edu/ 588 TIGR  ... 
doi:10.1093/nar/gki139 pmid:15608247 pmcid:PMC540093 fatcat:5m4ku2nytzewxipr56edceiwx4

Bioinformatic Tools for Inferring Functional Information from Plant Microarray Data II: Analysis Beyond Single Gene

Issa Coulibaly, Grier P. Page
2008 International Journal of Plant Genomics  
While it is possible to interpret microarray experiments a single gene at a time, most studies generate long lists of differentially expressed genes whose interpretation requires the integration of prior  ...  This prior knowledge is stored in various public and private databases and covers several aspects of gene function and biological information.  ...  PhytoProt (http://urgi.versailles.inra.fr/phytoprot) is a database of clusters of all the plants full-length protein sequences retrieved from SwissProt/TrEMBL.  ... 
doi:10.1155/2008/893941 pmid:18615189 pmcid:PMC2443398 fatcat:nvqj4qu6tfhatghnzofvebf7sm

Unique genes in plants: specificities and conserved features throughout evolution

David Armisén, Alain Lecharny, Sébastien Aubourg
2008 BMC Evolutionary Biology  
Plant unique genes may also have homologs in bacteria and we showed a link between the targeting towards plastids of proteins encoded by plant nuclear unique genes and their homology with a bacterial protein  ...  Plant genomes contain a high proportion of duplicated genes as a result of numerous whole, segmental and local duplications.  ...  Acknowledgements We are grateful to Jean-Loup Risler for providing A. thaliana unique genes defined in the PHYTOPROT resource and Vincent Thareau for providing PFAM motifs for O. lucimarinus and P. patens  ... 
doi:10.1186/1471-2148-8-280 pmid:18847470 pmcid:PMC2576244 fatcat:jj6zzrewlfg2nhftoopvyhqb64

GeneFarm, structural and functional annotation of Arabidopsis gene and protein families by a network of experts

S. Aubourg
2004 Nucleic Acids Research  
ª 2005, the authors  ...  The purpose of the GeneFarm project is to obtain homogeneous, reliable, documented and traceable annotations for Arabidopsis nuclear genes and gene products, and to enter them into an added-value database  ...  The GeneFarm database has been filed at the 'Agence pour la  ... 
doi:10.1093/nar/gki115 pmid:15608279 pmcid:PMC540069 fatcat:5i6iv33sffhmdgzsbedb2ggtpa

BioMOBY Successfully Integrates Distributed Heterogeneous Bioinformatics Web Services. The PlaNet Exemplar Case

M. Wilkinson
2005 Plant Physiology  
deployed to integrate the on-line plant genome databases and analytical services provided by a European consortium of databases and data service providers.  ...  BioMOBY is a biological Web Service interoperability initiative that began as a retreat of representatives from the model organism database community in September, 2001.  ...  Complex workflow examples are available from the PlaNet Web site (http:// www.eu-plant-genome.net), e.g. implementing questions like ''What Arabidopsis genes from the NBS-LRR family, as defined by a Phytoprot  ... 
doi:10.1104/pp.104.059170 pmid:15888673 fatcat:wlmqu4vpfzcffk7rg3bjzt3ita