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A Database for Transcription Factor Prediction in Medicago truncatula

The study of transcription factors plays an important role in the understanding of the molecular mechanism of gene regulation as a whole in plants. While several transcription factor databases of Arabidopsis have being actively developed, there is no reported work on the model legume species, Medicago truncatula, of which the gene-space genomic sequencing will be completed in the near future.

We developed a pipeline and a relational database for the prediction of Medicago truncatula transcription factors. The prediction was based on transcription factor binding sites and Hidden Markov Models (HMM). The models were built mainly on documented transcription factors and their family information in Arabidopsis and a small number of known transcription factors from legume (soybean, Alfalfa and Medicago truncatula). The prediction was made on the putative genes released by the International Medicago Genome Annotation Group (IMGAG). The prediction results were further grouped into multiple families and sub-families according to the classification of their functions. We also annotated a number of transcription factors that are related to nodule mechanism. The pipeline is being periodically executed to synchronize with the monthly release of IMGAG gene calls and daily update of Medicago truncatula genomic assembly.

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Copyright © 2007 by The Samuel Roberts Noble Foundation, Inc.