| Abstract Detail
Bioinformatics - Afternoon Traini, Alessandra [1], Chiusano, Maria Luisa [1]. Mapping expressed sequence onto genomic data: evaluation of tools for a reliable experimental annotation. CURATED gene annotation is a challenging computational problem in genomics. Many standalone programs are available for spliced aligning expressed sequence tags onto a genome sequence. With the aim to contribute to the bioinformatics efforts of the Tomato Genome Sequencing project we tested the software proposed by the International Committee for cDNA/EST to genome mapping. We investigated which algorithm is more reliable and in which context, comparing and evaluating some of the most frequently used specialized software, to provide a reference for the annotation of Tomato Gene Models. We tested sim4 [1], based on the BLASTZ algorithm [2], Galahad, included in the grail-exp package [3], blEST [1] and SIBsim4 [1], all based on sim4 algorithm [1], and GeneSeqer [4][5] as software commonly proposed as solving the task of mapping cDNAs/ESTs to genomic sequences. To provide a reliable informative benchwork for Tomato genome annotation based on experimental results, we set up a Gbrowse based platform reporting the results from the different methods. The datasets used in the present analysis are the Tomato expressed sequences available from dbEST and from the genome sequencing effort at the SOL Genomics Network. We present here the results of our evaluation of the software considered and we propose multiple algorithm usage under different constraints to provide exhaustive and reliable information when experimentally annotating genome sequence data. 1 L. Florea, et al. Genome Research (1998). 2 S. Schwartz, et al. Genome Research (2003).3 D. Hyatt, et al. Genome Sequencing and Biology Meeting May 2000. 4 V. Brendel, et al. Bioinformatics (2004). 5 D. Shannon, et al. Nucleic Acids Research (2003). Acknowledgements Work supported by the Agronanotech Project (Ministry of Agriculture, Italy).
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1 - University Federico II of Naples, Structural and Functional Biology, , Italy
Keywords:
none specified
Session: SAT07-3
Location: Hall of Ideas Room E/Monona Terrace
Date: Wednesday, July 26th, 2006
Time: 2:40 PM
Abstract ID:89 |
