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AgBase

AgBase is a curated, open-source, web-accessible resource for functional analysis of agricultural plant and animal gene products.  AgBase is hosted and supported, in part, by the IGBB.  The AgBase team consists of biocurators and computational biologists under the direction of Dr. Fiona M. McCarthy.  The long-term goal of AgBase is to serve the needs of agricultural research communities by facilitating genome annotation for agriculture researchers and for those researchers primarily using agricultural species as biomedical models. 

AgBase serves as home to and/or is integrated with a number of species/subject-specific databases including the following:  

Bovine Genome Atlas

The Bovine Gene Atlas (BGA) is a compendium of over 7.2 million unique 20 base transcript tags profiled from 81 tissues acquired from the cow Dominette 01449, her male fetus, her 255 day old heifer calf, and her father.

Bird Base

Bird Base is a genomics database devoted to the class Aves.  Birds serve as model organisms important to the study of neurobiology, immunology, genetics, development, oncology, virology, cardiovascular biology, evolution and a variety of other life sciences. Many bird species are also important to agriculture, providing an enormous worldwide food source. Genomic approaches are proving invaluable to studying traits that affect meat yield, disease resistance, behavior, and bone development along with many other factors affecting productivity. In this context, BirdBase serves both biomedical and agricultural researchers. 

Chicken Gene Nomenclature Consortium 

The Chicken Gene Nomenclature Consortium (CGNC) is an international group of researchers interested in providing standardized gene nomenclature for chicken genes. A Chicken Gene Annotation Tool is available from CGNC-UK which assigns chicken nomenclature based on predicted orthology to human genes. The CGNC-US database includes CGNC-UK information and adds manually biocurated genes from professional biocurators and interested contributors. Both resources are part of a united CGNC effort and nomenclature data is shared and coordinated between these two resources.

Corn Fungal Resistance Associated Sequences Database 

Corn Fungal Resistance Associated Sequences Database (CFRAS-DB) is a relational database with dynamic querying and data integration that can be used by researchers to identify genetic sequences with a high probability of being associated with aflatoxin accumulation resistance, according to multiple lines of evidence. CFRAS-DB integrates genomic, proteomic, and genetic data from multiple studies in maize dealing with aflatoxin accumulation or Aspergillus flavus resistance.

Host-Pathogen Interaction Database

The Host-Pathogen Interaction Database (HPIDB) is a genomics resource devoted to understanding molecular interactions between key organisms and the pathogens to which they are susceptible.

Fellows & Affiliates Spotlight
Din-Pow Ma
Dr. Din-Pow Ma
Professor
Biochemistry, Molecular Biology, Entomology & Plant Pathology
IGBB Affiliate
email
(662) 325-2640
website
Rama Nannapaneni
Dr. Ramakrishna (Rama) Nannapaneni
Associate Research Professor
Food Science, Nutrition & Health Promotion
IGBB Affiliate
email
(662) 325-7697
website

Research Spotlight


Topic:
Cotton diversity

IGBB Scientists:
Daniel Peterson
Tony Arick
Kurt Showmaker

Funding:
USDA

The IGBB is supported, in part, by the following units:


The IGBB is an HPC² member center.