Reranking candidate gene models with cross-species comparison for improved gene prediction
نویسندگان
چکیده
منابع مشابه
AGenDA: gene prediction by cross-species sequence comparison
Automatic gene prediction is one of the major challenges in computational sequence analysis. Traditional approaches to gene finding rely on statistical models derived from previously known genes. By contrast, a new class of comparative methods relies on comparing genomic sequences from evolutionary related organisms to each other. These methods are based on the concept of phylogenetic footprint...
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Many genes and biological processes function in similar ways across different species. Cross-species gene expression analysis, as a powerful tool to characterize the dynamical properties of the cell, has found a number of applications, such as identifying a conserved core set of cell cycle genes. However, to the best of our knowledge, there is limited effort on developing appropriate techniques...
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Sequencing of large fragments of genomic DNA makes it possible to perform comparisons of genomic sequences for identification of protein-coding regions. We have conducted a comparative analysis of homologous genomic sequences of organisms with different evolutionary distances and determined the degree of conservation of the non-coding regions between closely related organisms. In contrast, more...
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Genes differentially expressed by tumor cells represent promising drug targets for anti-cancer therapy. Such candidate genes need to be validated in appropriate animal models. This study examined the suitability of rodent models of bladder cancer in B6D2F1 mice and Fischer-344 rats to model clinical bladder cancer specimens in humans. Using a global gene expression approach cross-species analys...
متن کاملComparison of gene prediction algorithms
All three approaches share a number of common properties, which we list before going on to explore their differences: • Most algorithms locate protein-coding regions as opposed to whole genes. Nevertheless “gene prediction” remains standard nomenclature. • There is a significant amount of application-specific knowledge going into these designs. Of the systems referenced here only VEIL comes clo...
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ژورنال
عنوان ژورنال: BMC Bioinformatics
سال: 2008
ISSN: 1471-2105
DOI: 10.1186/1471-2105-9-433