| Abstract Detail
Potato Genomics - Afternoon De Koeyer, David [1], Griffiths, Rebecca [2], Lagüe, Martin [1], Kloosterman, Bjorn [3], Bachem, Christian [4], Flinn, Barry [5]. Bioinformatics analyses of potato ESTs for an international potato oligonucleotide microarray chip consortium (POCI). POTATO (Solanum tuberosum) currently has the largest number of publicly available expressed sequence tag (EST) sequences of all Solanaceae species (http://www.ncbi.nlm.nih.gov/dbEST/dbEST_summary.html). Most of these ESTs, plus other proprietary sequences were combined and used to generate a unigene assembly. Sequences were contributed by The Institute for Genomics Research (TIGR), the Canadian Potato Genome Project (CPGP), Aalborg University, Agriculture and Agri-Food Canada, IPK-Gaterslaben, and Wageningen University. To efficiently process each of the ESTs, an automated pipeline was created to clean, assemble, and annotate each sequence. The initial set of 220,650 sequences produced 45,754 unigenes. These unigenes were used to design an Agilent 44K 60-mer oligo potato array. BLAST and Gene Ontology annotations have been determined for all features on the array. We will present an overview of bioinformatics pipeline used to create potato unigene set, summarize the annotation results, and discuss opportunities for collaboration in bioinformatics to mine the data generated by microarray experiments with the POCI chip. Details of the unigene assembly can be found on the CPGP website (http://www.cpgp.ca/Resources/micro/description.html).
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Description of POCI array
1 - Agriculture and Agri-Food Canada, Potato Research Centre, P.O. Box 20280, 850 Lincoln Rd, Fredericton, NB, E3B 4Z7, Canada
2 - Genome Atlantic, 921 College Hill Road, Fredericton, NB, E3B 6Z9, Canada
3 - Wageningen University, Plant Sciences, Droevendaalsesteeg 1, Wageningen, 6700 AJ, The Netherlands
4 - Wageningen University, Plant Breeding, Droevendaalsesteeg 1, Wageningen, 6700 AJ, The Netherlands
5 - Institute for Sustainable and Renewable Resources, 150 Slayton Ave, Danville, VA, 24540, USA
Keywords:
Potato
Bioinformatics
microarray.
Session: SAT09-3
Location: Hall of Ideas Room I/Monona Terrace
Date: Wednesday, July 26th, 2006
Time: 1:50 PM
Abstract ID:365 |
