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Bioinformatics and Computational Biology Summer Institute |
Research Projects for Fellows, June 20 - August 6, 2005
P3: Development of a workflow to populate a synteny browser database
| Title: | Development of a workflow to populate a synteny browser database. |
| Mentors: | Dr. Xioakang Pan and Dr. Volker Brendel |
| Description: | SynBrowse (Synteny Browser) is a generic sequence comparison tool for visualizing genome alignments both within and between species, recently developed by Dr. Xiaokang Pan. The tool helps scientists study and analyze colinearity of genes on different chromosomal regions (macro-synteny and micro-synteny)and identify other conserved elements between sequences. This software is particularly useful for studying genome duplication and evolution. It can also aid in identifying uncharacterized genes, putative regulatory elements and novel structural features of study species by comparing to a well-annotated reference sequence, thus enabling genome curators to refine and edit annotations of species that have incomplete genome annotations. The intern(s) will work with Dr. Pan to build workflows that populate the underlying databases. The workflows will use existing software for gene structure prediction. Some familiarity with Linux and Perl will be required for this project. |
| Web Resources: | SynBrowse PlantGDB |
| References: | Dong, Q., Schlueter, S.D. & Brendel, V. (2004) PlantGDB, plant genome database and analysis tools. Nucl. Acids Res. 32, D354-D359. |