Bioinformatics.fr

Share a resource

Gramene

http://www.gramene.org/ Gramene is a curated, open-source, data resource for comparative genome analysis in the grasses. Our goal is to facilitate the study of cross-species homology relationships using information derived from public projects involved in genomic and EST sequencing, protein structure and function analysis, genetic and physical mapping, interpretation of biochemical pathways, gene and QTL localization and descriptions of phenotypic characters and mutations.

Maize Genetics and Genomics Database

http://www.maizegdb.org/

Description :
A central repository for public maize information.

Cereal Small RNA Database

http://sundarlab.ucdavis.edu/smrnas/

Description :
Small RNAs (smRNAs), which include microRNAs (miRNAs), small-interfering RNAS (siRNAs) and trans-acting siRNAs (ta-siRNAs) are ~19-24 nt RNAs that are important negative regulators of nucleotide sequences involved in development, homeostasis and in the maintenance of heterochromatic states. The Cereals Small RNA Database (CSRDB) is an integrated resource for small RNAs expressed in rice and maize that includes a genome browser and a smRNA-target relational database as well as relevant bioinformatic tools. The resource currently contains a preliminary dataset of 35,454 and 68,871 mapped smRNA sequence reads for rice and maize respectively. Future updates will include smRNA data derived from different tissues and conditions. The database is accessible online at http://sundarlab.ucdavis.edu/smrnas/.

POGs/PlantRBP

http://plantrbp.uoregon.edu/

Description :
POGs/PlantRBP (http://plantrbp.uoregon.edu/) is a relational database that integrates data from rice, Arabidopsis, and maize by placing the complete Arabidopsis and rice proteomes and available maize sequences into "putative orthologous groups" (POGs). Annotation efforts will focus on predicted RNA binding proteins (RBPs): i.e. those with known RNA binding domains or otherwise implicated in RNA function. POGs form the heart of the database, and were assigned using a mutual-best-hit-strategy after performing BLAST comparisons of the predicted Arabidopsis and rice proteomes. Each POG entry includes orthologs in Arabidopsis and rice, annotated with domain organization, gene models, phylogenetic trees, and multiple intracellular targeting predictions. A graphical display maps maize sequences on to their most similar rice gene model. The database can be queried using any combination of gene name, accession, domain, and predicted intracellular location, or using BLAST. Useful features of the database include the ability to search for proteins with both a specified domain content and intracellular location, the concurrent display of mutual best hits and phylogenetic trees which facilitates evaluation of POG assignments, the association of maize sequences with POGs, and the display of targeting predictions and domain organization for all POG members, which reveals consistency (or lack thereof) of those predictions.

Aknowledgement :
This work was supported by grant DBI-0421799 from the National Science Foundation.

MaizeGDB

http://www.maizegdb.org/

Description :
The Maize Genetics and Genomics Database (MaizeGDB) is a central repository for maize sequence, stock, phenotype, genotypic and karyotypic variation, and chromosomal mapping data. In addition, MaizeGDB provides contact information for over 2,400 maize cooperative researchers, facilitating interactions among members of the rapidly expanding maize community. MaizeGDB represents the synthesis of all data available previously from ZmDB and from MaizeDB - databases that have been superseded by MaizeGDB. MaizeGDB provides web-based tools for ordering maize stocks from several organizations including the Maize Genetics Cooperation Stock Center and the North Central Regional Plant Introduction Station (NCRPIS). Sequence searches yield records displayed with embedded links to facilitate ordering cloned sequences from various groups including the Maize Gene Discovery Project and the Clemson University Genomics Institute (CUGI). An intuitive web interface is implemented to facilitate navigation among related data, and analytical tools are embedded within data displays. Web-based curation tools for both designated experts and general researchers facilitate community-aided data acquisition.

Recent develoments :
MaizeGDB is actively expanding the scope of the database to include novel data types. For example, MaizeGDB now includes chromosome images from cytogenic FISH mapping.

Aknowledgement :
MaizeGDB is funded by the USDA-ARS Specific Cooperative Agreement No. 58-3625-1-192.

References :
1. Lawrence, C.J, Dong, Q., Polacco, M.L., Seigfried, T.E. and Brendel, V. (2004) MaizeGDB, the community database for maize genetics and genomics. Nucleic Acids Research, 32, in press.

PANZEA

http://www.panzea.org/

Description :
Serving as a community resource, Panzea (http://www.panzea.org) is the bioinformatics arm of the Molecular and Functional Diversity in the Maize Genome project. Maize, a classical model for genetic studies, is an important crop species and also the most diverse crop species known. On average, two randomly chosen maize lines have one SNP every ~100 bp; this divergence is roughly equivalent to the differences between humans and chimpanzees. This exceptional genotypic diversity underlies the phenotypic diversity maize needs to be cultivated in a wide range of environments. The Molecular and Functional Diversity in the Maize Genome project aims to understand how selection has shaped molecular diversity in maize and then relate molecular diversity to functional phenotypic variation. The project will screen 4000 loci for the signature of selection and create a wide range of maize and maize-teosinte mapping populations. These populations will be genotyped and phenotyped, permitting high-power and high-resolution dissection of the traits and relating the molecular diversity to functional variation. Panzea provides access to the genotype, phenotype, and polymorphism data produced by the project through user-friendly web-based database searches and data retrieval/visualization tools, as well as a wide variety of information and services related to maize diversity.

Aknowledgement :
We thank all members of the Molecular and Functional Diversity in the Maize Genome project for providing data, educational materials, and/or technical support for Panzea. This work is supported by NSF Grant 0321467 and USDA ARS.

TIGR Maize database

http://maize.tigr.org/

Description :
The TIGR Maize Database is a repository of publicly available maize genomic sequences, we have created the TIGR Maize Database (http://maize.tigr.org). In this resource, we have assembled approximately 900,000 gene-enriched reads into Assembled Zea mays (AZM) sequences. The sequences are annotated and anchored to maize chromosomes using available sequenced markers. The database also contains a maize repeat database and the draft sequence assemblies of 287 maize BAC clones, which we annotated along with 172 additional publicly available BAC clones. All sequences, assemblies and annotations are available at the project web site via web interfaces and FTP downloads.

Aknowledgement :
We thank the participants of the Consortium for Maize Genomics project (Robert Citek, Muhammad Budiman, Andrew Nunberg, Joseph Bedell, Nathan Lakey, and Karel Schubert; http://maize.danforthcenter.org) for their valuable contributions. This work was supported by National Science Foundation award DBI-0221536.

Plant Ontology database

http://www.plantontology.org/

Description :
The Plant Ontology (PO, http://www.plantontology.org) is a collaborative effort among several plant databases and experts in plant systematics, botany and genomics. The goal of the PO is to develop simple yet robust and extensible controlled vocabularies that accurately reflect the biology of plant structures (morphology and anatomy) and developmental stages. Once implemented, these provide a network of vocabularies linked by relationships (ontology) to facilitate queries that cut across data sets within a database or between multiple databases. Using the ontology browser (http://www.plantontology.org/amigo/go.cgi), over 5000 gene annotations from Arabidopsis, maize and rice can be searched. Using the same browser a user can also search the plant structure (e.g. root hair) and growth stage (e.g. reproductive stage) terms. Learn how to browse and use the ontologies by visiting http://www.plantontology.org/docs/otherdocs/tutorials.html. The vocabularies, annotations, mappings and the database can be downloaded by following the instructions provided at http://www.plantontology.org/download/download.html. Learn more about the ontologies, design and development aspects by visiting http://www.plantontology.org/docs/docs.html

Recent develoments :
The current version of the ontology integrates diverse vocabularies used to describe Arabidopsis, maize, rice, Triticeae, legumes and tomato plant anatomy, morphology, growth and developmental stages. Using the ontology browser (http://www.plantontology.org/amigo/go.cgi), over 5000 gene annotations from three species specific databases, The Arabidopsis Information Resource (TAIR, http://www.arabiidopsis.org) for Arabidopsis, Gramene (http://www.gramene.org) for rice and MaizeGDB (http://www.maizegdb.org) for maize, can now be queried and retrieved.

Aknowledgement :
We gratefully acknowledge the Gene Ontology Consortium for making the ontology browser (AmiGO), editor (DAG-Edit), Obol tool and database software available and for help with modifications and implementation. We are grateful to many researchers, reviewers, database groups and curators for help in reviewing, adding new terms to the ontology and using them in their annotation work. This work is supported by the National Science Foundation award (Grant No. 0321666) to the Plant Ontology Consortium and USDA-ARS, USA.

References :
1. The Plant Ontology Consortium. (2002) The Plant Ontology Consortium and Plant Ontologies. Comparative and Functional Genomics, 3: 137-142.
2. P. Jaiswal, S. Avraham, K. Ilic, E.A. Kellogg, A. Pujar, L. Reiser, R.Y. Seung, M.M. Sachs, M. Schaeffer, L. Stein et al. (2005) Plant Ontology (PO): a controlled vocabulary of plant structures and growth stages. Comparative and Functional Genomics, 6: 388-397.

Cancel