Open Access Highly Accessed Database

AgBase: a functional genomics resource for agriculture

Fiona M McCarthy17*, Nan Wang27, G Bryce Magee27, Bindu Nanduri17, Mark L Lawrence1, Evelyn B Camon3, Daniel G Barrell3, David P Hill4, Mary E Dolan4, W Paul Williams5, Dawn S Luthe67, Susan M Bridges27 and Shane C Burgess17

Author Affiliations

1 Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, P.O. Box 1600, Mississippi State, MS 39762, USA

2 Department of Computer Science and Engineering, Bagley College of Engineering, P.O. Box 9637, Mississippi State University, MS 39762, USA

3 European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK

4 Mouse Genome Informatics, The Jackson Laboratory 600 Main Street, Bar Harbor, ME 04609, USA

5 USDA ARS Corn Host Plant Resistance Research Unit, Box 5367, Mississippi State University, MS 39762, USA

6 Department of Biochemistry and Molecular Biology, P.O. Box 9650, Mississippi State University, MS 39762, USA

7 Institute for Digital Biology, Mississippi State University, MS 39762, USA

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BMC Genomics 2006, 7:229  doi:10.1186/1471-2164-7-229

Published: 8 September 2006

Additional files

Additional File 1:

Entity relationship (ER) model of the AgBase database. The AgBase schema design is protein centric. In addition to the taxonomy identifier, sequence, and GO annotations, mappings to number of identifiers are maintained for each protein.

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Open Data

Additional File 2:

ePSTs identified from P. multocida using the proteogenomic pipeline developed at AgBase. P. multocida Pm70 ePSTs identified by proteogenomic mapping. For all 202 ePSTS the original MS peptide and its length, the extended ePST and its length as well as the genome start and end positions of the ePST are shown.

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Open Data

Additional File 3:

Location of ePST47 in P. multocida Pm70 genome. Region of PM70 genome coding for accA and guaA genes and the 5' end of PMO291 (A). The position in genome is on the left hand side; DNA sequence is shown above; amino acid sequence below; direction of reading frames shown by arrows. The ePST47 is located in the intergenic region between accA and guaA. The figure is taken directly from NCBI nucleotide database graph view with the accession number NC_002663. An expanded view of intergenic region between accA and guaA including ePST47, which runs in the opposite direction to accA, guaA and PMO291 (arrowed) is also shown (B). The overlapping peptides used to identify ePST47 are indicated using bold type (PRIDE accession number pending). This region of the PM70 genome also has 60% identity (* indicates identical nucleotides) and 74% similarity at the protein level with the Haemophilus ducreyi hypothetical protein HD_1218 (Genbank accession AAP96060).

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Open Data

Additional File 4:

Channel catfish proteins and ESTs identified using the ProtIDer tool. The ProtIDer tool is designed for use with species that have large numbers of ESTs but few proteins in the NRPD. ProtIDer matches ESTs and EST assemblies to highly homologous proteins from other species by TBLASTN-searching the NRPD with all catfish ESTs. For example, the channel catfish genome sequence is not available and there are only 1,108 NRPD entries for this species. When we analyzed channel catfish ovary tissue we were only able to identify 10 proteins from NRPD. Using ProtIDer to create a database of highly homologous proteins resulted in a five-fold increase in the number of proteins identified in this experiment. The proteins identified from the channel catfish NRPD database (cfNRPD), highly homologous database (hpDB) and EST databases are shown here. The ProtIDer tool is available from AgBase upon request.

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Open Data