Research Projects for Fellows, 2009
P02: Gene structure evaluation and dissemination of gene models
| Short Title: |
Gene structure evaluation and dissemination of gene models |
| Mentors: |
Dr. Volker Brendel |
| Description: |
As discussed in the short course, eukaryotic gene structure prediction remains
a difficult task that is only partially solved by computer programs and often needs human curation.
The scope of this project is to explore "divide-and-conquer" strategies to approach this problem: for a
given set of gene structure annotations, we define various scores that summarize the match of the
annotation with currently available transcript evidence (GAEVAL pages on the PlantGDB xGDB genome browsers).
We would like to use these scores to distinguish different sets of annotations: those with perfect evidence, those in need of simple corrections, those with complex patterns, and others. For some of these models, yrGATE can be used to define corrected gene models. As part of this project, we will develop software to map community-contributed gene structure annotations to different versions of the relevant genome assembly (with possibly changed coordinate system). The project would be appropriate for a student with some programming background (Perl would be a plus) who'd wish to gain hands-on experience with bioinformatic tool development. Successful completion of the project should lead to publication and distribution of the software.
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| Web Resources: |
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| References: |
Wilkerson, M.D., Schlueter, S.D. & Brendel, V. (2006) yrGATE: a web-based gene-structure annotation tool for the identification and dissemination of eukaryotic genes. Genome Biol. 7 , R58. [ PubMed ID: 16859520 ] [ PDF ] |
| Suitable background skills: |
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