Dataset Information

Assessing the impact of comparative genomic sequence data on the functional annotation of the Drosophila genome.

ABSTRACT: BACKGROUND:It is widely accepted that comparative sequence data can aid the functional annotation of genome sequences; however, the most informative species and features of genome evolution for comparison remain to be determined. RESULTS:We analyzed conservation in eight genomic regions (apterous, even-skipped, fushi tarazu, twist, and Rhodopsins 1, 2, 3 and 4) from four Drosophila species (D. erecta, D. pseudoobscura, D. willistoni, and D. littoralis) covering more than 500 kb of the D. melanogaster genome. All D. melanogaster genes (and 78-82% of coding exons) identified in divergent species such as D. pseudoobscura show evidence of functional constraint. Addition of a third species can reveal functional constraint in otherwise non-significant pairwise exon comparisons. Microsynteny is largely conserved, with rearrangement breakpoints, novel transposable element insertions, and gene transpositions occurring in similar numbers. Rates of amino-acid substitution are higher in uncharacterized genes relative to genes that have previously been studied. Conserved non-coding sequences (CNCSs) tend to be spatially clustered with conserved spacing between CNCSs, and clusters of CNCSs can be used to predict enhancer sequences. CONCLUSIONS:Our results provide the basis for choosing species whose genome sequences would be most useful in aiding the functional annotation of coding and cis-regulatory sequences in Drosophila. Furthermore, this work shows how decoding the spatial organization of conserved sequences, such as the clustering of CNCSs, can complement efforts to annotate eukaryotic genomes on the basis of sequence conservation alone.

SUBMITTER: Bergman CM

PROVIDER: S-EPMC151188 | biostudies-literature | 2002

REPOSITORIES: biostudies-literature

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Assessing the impact of comparative genomic sequence data on the functional annotation of the Drosophila genome.

Bergman Casey M CM Pfeiffer Barret D BD Rincón-Limas Diego E DE Hoskins Roger A RA Gnirke Andreas A Mungall Chris J CJ Wang Adrienne M AM Kronmiller Brent B Pacleb Joanne J Park Soo S Stapleton Mark M Wan Kenneth K George Reed A RA de Jong Pieter J PJ Botas Juan J Rubin Gerald M GM Celniker Susan E SE

Genome biology 20021230 12

<h4>Background</h4>It is widely accepted that comparative sequence data can aid the functional annotation of genome sequences; however, the most informative species and features of genome evolution for comparison remain to be determined.<h4>Results</h4>We analyzed conservation in eight genomic regions (apterous, even-skipped, fushi tarazu, twist, and Rhodopsins 1, 2, 3 and 4) from four Drosophila species (D. erecta, D. pseudoobscura, D. willistoni, and D. littoralis) covering more than 500 kb of ...[more]

PMID: 12537575

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Project description:During the last decade, a great number of extremely valuable large-scale genomics and proteomics datasets have become available to the research community. In addition, dropping costs for conducting high-throughput sequencing experiments and the option to outsource them considerably contribute to an increasing number of researchers becoming active in this field. Even though various computational approaches have been developed to analyze these data, it is still a laborious task involving prudent integration of many heterogeneous and frequently updated data sources, creating a barrier for interested scientists to accomplish their own analysis.We have implemented Dintor, a data integration framework that provides a set of over 30 tools to assist researchers in the exploration of genomics and proteomics datasets. Each of the tools solves a particular task and several tools can be combined into data processing pipelines. Dintor covers a wide range of frequently required functionalities, from gene identifier conversions and orthology mappings to functional annotation of proteins and genetic variants up to candidate gene prioritization and Gene Ontology-based gene set enrichment analysis. Since the tools operate on constantly changing datasets, we provide a mechanism to unambiguously link tools with different versions of archived datasets, which guarantees reproducible results for future tool invocations. We demonstrate a selection of Dintor's capabilities by analyzing datasets from four representative publications. The open source software can be downloaded and installed on a local Unix machine. For reasons of data privacy it can be configured to retrieve local data only. In addition, the Dintor tools are available on our public Galaxy web service at http://dintor.eurac.edu .Dintor is a computational annotation framework for the analysis of genomic and proteomic datasets, providing a rich set of tools that cover the most frequently encountered tasks. A major advantage is its capability to consistently handle multiple versions of tool-associated datasets, supporting the researcher in delivering reproducible results.

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Dataset Information

Assessing the impact of comparative genomic sequence data on the functional annotation of the Drosophila genome.

Publications

Assessing the impact of comparative genomic sequence data on the functional annotation of the Drosophila genome.

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