METHODS

Data sources

Currently, PIGD includes the following five organisms - Sorghum bicolor, Zea mays, Setaria italica, Panicum virgatum and Brachypodium distachyon. All genome data were downloaded from the Phytozome database (release version 9.1) [1].

Identification of Poaceae Intronless Genes

A stringent protocol was used to reliably identify Poaceae intronless genes. First, using the Java program, we extracted genes that contain a “CDS” line in GFF3 format files. Redundant sequences representing the same gene loci were then excluded. Finally, we retained sequences assembled into chromosomes for Sorghum bicolor, Zea mays and Brachypodium distachyon. Organelle sequences were discarded to avoid ambiguity. Scaffolds that could not be physically anchored in Setaria italica and Panicum virgatum were present in the data set. Thus, lists of non-redundant intronless genes from the five Poaceae organisms were generated.

Data assembly

Each entry into the PIGD integrated a comprehensive list of annotations on:

Comparisons between Poaceae species

The records contained within the “Comparison” menu were grouped into eight general classes of related information:

The PIGD web interface

A web-based platform, the PIGD combined the MySQL (version 5.5.8) database management system with a dynamic web interface based on PHP (version 5.3.3) and Javascript (version 1.2).

References

[1] Goodstein, D.M., Shu, S., Howson, R., et al. Phytozome: a comparative platform for green plant genomics. Nucleic Acids Res, 40, D1178-1186.
[2] Punta, M., Coggill, P.C., Eberhardt, R.Y., et al. The Pfam protein families database. Nucleic Acids Res, 40, D290-301.
[3] Artimo, P., Jonnalagedda, M., Arnold, K., et al. ExPASy: SIB bioinformatics resource portal. Nucleic Acids Res, 40, W597-603.
[4] Jensen, L.J., Gupta, R., Staerfeldt, H.H., et al. (2003) Prediction of human protein function according to Gene Ontology categories. Bioinformatics, 19, 635-642.
[5] Horton, P., Park, K.J., Obayashi, T., et al. (2007) WoLF PSORT: protein localization predictor. Nucleic Acids Res, 35, W585-587.
[6] Wheeler, D.L., Barrett, T., Benson, D.A., et al. (2005) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res, 33, D39-45.