PineappleDB: an online pineapple bioinformatics resource.
BACKGROUND
A world first pineapple EST sequencing program has been undertaken to investigate genes expressed during non-climacteric fruit ripening and the nematode-plant interaction during root infection. Very little is known of how non-climacteric fruit ripening is controlled or of the molecular basis of the nematode-plant interaction. PineappleDB was developed to provide the research community with access to a curated bioinformatics resource housing the fruit, root and nematode infected gall expressed sequences.


METHODS
PineappleDB is an online, curated database providing integrated access to annotated expressed sequence tag (EST) data for cDNA clones isolated from pineapple fruit, root, and nematode infected root gall vascular cylinder tissues. The database currently houses over 5600 EST sequences, 3383 contig consensus sequences, and associated bioinformatic data including splice variants, Arabidopsis homologues, both MIPS based and Gene Ontology functional classifications, and clone distributions. The online resource can be searched by text or by BLAST sequence homology. The data outputs provide comprehensive sequence, bioinformatic and functional classification information.


CONCLUSIONS
The online pineapple bioinformatic resource provides the research community with access to pineapple fruit and root/gall sequence and bioinformatic data in a user-friendly format. The search tools enable efficient data mining and present a wide spectrum of bioinformatic and functional classification information. PineappleDB will be of broad appeal to researchers investigating pineapple genetics, non-climacteric fruit ripening, root-knot nematode infection, crassulacean acid metabolism and alternative RNA splicing in plants.
Moyle
Richard L
RL
Department of Botany, University of Queensland, QLD 4072, Brisbane, Australia. r.moyle1@mailbox.uq.edu.au
Crowe
Mark L
ML
Ripi-Koia
Jonni
J
Fairbairn
David J
DJ
Botella
José R
JR
D017398:Alternative Splicing / Q000235:genetics; D031230:Ananas / Q000235:genetics*; D019295:Computational Biology; D016384:Consensus Sequence; D030561:Databases, Nucleic Acid; D020224:Expressed Sequence Tags; D005638:Fruit / Q000235:genetics; D017238:Genes, Helminth; D020407:Internet; D018517:Plant Roots / Q000235:genetics; D012689:Sequence Homology, Nucleic Acid