AlfalfaTFDB was generated in the Nemchinov laboratory by a genome-wide profiling using the allele-aware chromosome-level alfalfa genome assembly downloaded from https://figshare.com/projects/whole_genome_sequencing_and_assembly_of_Medicago_sativa/66380 The putative encoded protein sequences were submitted to PlantTFcat (http://plantgrn.noble.org/PlantTFcat/) and PlantTFDB (http://planttfdb.gao-lab.org/prediction_result.php) webservers and transcription factor domains were identified using InterProScan v. 5.44-79.0 (Jones et al. 2014) and ARS-SCINet (https://scinet.usda.gov). The results were consolidated and filtered for putative predicted transcription factors and agreement between prediction programs. For proteins with multiple domains, only the top domain was extracted for each sequence.
Transcription factors in Medicago sativa, computationally predicted by a genome-wide profiling (browse by family)
Return to Alfalfa Transcription Factor Resource Center
How to Cite:
1. Nemchinov L.G., Shao J., Grinstead S., Postnikova O.A. (2021) Transcription Factors in Alfalfa (Medicago sativa L.): Genome-Wide Identification and a Web Resource Center AlfalfaTFDB. In: Yu LX., Kole C. (eds) The Alfalfa Genome. Compendium of Plant Genomes. Springer, Cham, Switzerland, p.111-128. link
2. Postnikova OA, Shao, J and Nemchinov LG (2014). In silico identification of transcription factors in Medicago sativa using available transcriptomic resources. Molecular Genetics and Genomics.link
DOI 10.1007/s00438-014-0823-7, Epub 2014 Feb 21