| Abstract Detail
Bioinformatics - Afternoon Bruggmann, Remy [1], Buchan, Daniel [2], Abbott, James [2], Butcher, Sarah [2], Nicholson, Christine [3], McLaren, Karen [3], Humphray, Sean [3], Rogers, Jane [3], Bryan, Glenn [4], Seymour, Graham [5], Bishop, Gerard [6], Mayer, Klaus FX [1]. Annotation Tools and Annotation in the UK Tomato Chromosome 4. WITH the start of the whole genome sequencing of the tomato genome, appropriate analytical tools, analysis pipelines and strategies to annotate the genome are needed. Although there are numerous ab initio gene prediction programs available, for the time being none of them has currently been adapted and evaluated for Solanum lycopersicum. Complimentary to gene detection based on intrinsic data, the rich data resource on tomato and other plant transcriptomic data provide an important and valuable data resource for genome annotation. We have implemented a pipeline to use tomato and other plant-derived transcriptomic data for the structural gene annotation on tomato BAC sequences by the application of GenomeThreader (Gremme et al., 2005). Beside the application for gene calling complimentary to gene finder applications it also enables to conduct high quality EST-mappings to select genes for the inclusion into test/training data set for gene finder training purposes. In addition, we developed an adapter to the widely used 'Apollo Genome Annotation Curation Tool'. This adapter allows to directly retrieving data from a (genome)-database to visualize the EST-mappings and annotations. Apollo has been designed to curate (add/change) gene models according to the evidences (e.g. EST-mappings) retrieved from the database. This adapter is available for local use and as web-service for remote access. We analyzed all available BACs from tomato chromosome 4 applying this annotation pipeline and we will report on the current state of the annotation efforts with regard to the establishment of a test and training set for in silico gene finders. References:Gremme, G., Brendel, V., Sparks, M. E., and Kurtz, S. (2005). Engineering a software tool for gene structure prediction in higher organisms. Information and Software Technology 47, 965-978.
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1 - GSF Research Center for Environment and Health, MIPS/IBI Institute for Bioinformatics, Ingolstaedter Landstr. 1, Neuherberg, 85764, Germany
2 - Imperial College, Division of Molecular Biosciences, Faculty of Life Sciences, South Kensigton Campus, London, SW7 2AZ, United Kindom
3 - Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
4 - Scottish Crop Research Institute, Invergowrie, Dundee, DD2 5DA, UK
5 - University of Warwick, Warwick HRI, Wellesbourne, CV35 9EF, United Kindom
6 - Imperial College London, Division of Biology, Wye Campus, Wye , Ashford,, TN25 5AH, United Kindom
Keywords:
annotation
apollo
tomato
Bioinformatics.
Session: SAT07-4
Location: Hall of Ideas Room E/Monona Terrace
Date: Wednesday, July 26th, 2006
Time: 3:00 PM
Abstract ID:246 |
