Research Projects for Fellows, 2009
P01: Tools and applications for gene structure annotation
| Short Title: |
Tools and applications for gene structure annotation |
| Mentors: |
Dr. Volker Brendel |
| Description: |
In this project we'll seek enhancements to the yrGATE software for eukaryotic
protein coding gene structure annotation. Some enhancements concern the implementations of yrGATE on
the PlantGDB xGDB genome browsers we discussed in the short course. For example, it would be good to have a
threshold option that selects only very high quality spliced alignments for evidence-based exon definition.
More importantly, it is highly desirable to develop yrGATE extensions that connect tightly with non-xGDB
genome browsers, such as the widely used Gbrowse or Ensembl browsers. This 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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