PlantTribes -- a gene and gene family resource for comparative genomics in plants
What you can do:
A plant gene family database based on the inferred proteomes of five sequenced plant species: Arabidopsis thaliana, Carica papaya, Medicago truncatula, Oryza sativa and Populus trichocarpa.
Highlights:
- Species' protein-coding genes were classified into putative gene families, called tribes, using three clustering stringencies (low, medium and high). For all tribes, we have generated protein and DNA alignments and maximum-likelihood phylogenetic trees.
- A parallel database of microarray experimental results is linked to the genes, which lets researchers identify groups of related genes and their expression patterns.
- Unified nomenclatures were developed, and tribes can be related to traditional gene families and conserved domain identifiers.
- SuperTribes, constructed through a second iteration of MCL clustering, connect distant, but potentially related gene clusters.
- The global classification of nearly 200 000 plant proteins was used as a scaffold for sorting approximately 4 million additional cDNA sequences from over 200 plant species.
- All data and analyses are accessible through a flexible interface allowing users to explore the classification, to place query sequences within the classification, and to download results for further study.
Keywords:
- Databases, Genetic
- Genes, Plant
- Genome, Plant
- Plants/*classification
- Proteins/*classification/genetics
- Sequence Alignment
- Arabidopsis
- Carica papaya
- Medicago truncatula
- Oryza sativa
- Populus trichocarpa
Literature & Tutorials:
This record last updated: 04-10-2008