Liang, C., Mao, L., Ware, D. H., Stein, L. D. (October 2009) Evidence-based gene predictions in plant genomes. Genome Res, 19 (10). 1912-1923 .
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Abstract
Automated evidence-based gene building is a rapid and cost-effective way to provide reliable gene annotations on newly sequenced genomes. One of the limitations of evidence-based gene builders, however, is their requirement for transcriptional evidence - known proteins, full-length cDNAs, or ESTs - in the species of interest. This limitation is of particular concern for plant genomes, where the rate of genome sequencing is greatly outpacing the rate of EST- and cDNA-sequencing projects. To overcome this limitation, we have developed an evidence-based gene build system (the Gramene pipeline) that can use transcriptional evidence across related species. The Gramene pipeline uses the Ensembl computing infrastructure with a novel data processing scheme. Using the previously annotated plant genomes, the dicot and the monocot , we show that the cross-species ESTs from within monocot or dicot class are a valuable source of evidence for gene predictions. We also find that, using only EST and cross-species evidence, the Gramene pipeline can generate a plant gene set that is comparable in quality to the human genes based on known proteins and full-length cDNAs. We compare the Gramene pipeline to several widely used ab initio gene prediction programs in rice; this comparison shows the pipeline performs favorably at both the gene and exon levels with cross-species gene products only. We discuss the results of testing the pipeline on a 22-Mb region of the newly sequenced maize genome and potential application of the pipeline to other genomes.
| Item Type: | Paper |
|---|---|
| Subjects: | bioinformatics bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification bioinformatics > genomics and proteomics > genetics & nucleic acid processing bioinformatics > genomics and proteomics bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > genes, structure and function bioinformatics > genomics and proteomics > genetics & nucleic acid processing > genomes organism description > plant |
| CSHL Authors: | |
| Communities: | CSHL labs > Stein lab CSHL labs > Ware lab |
| Depositing User: | Matt Covey |
| Date: | October 2009 |
| Date Deposited: | 21 Feb 2013 16:22 |
| Last Modified: | 06 Nov 2017 17:14 |
| PMCID: | PMC2765265 |
| Related URLs: | |
| URI: | https://repository.cshl.edu/id/eprint/27372 |
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