1. University of Pittsburgh
Comparative genome sequence navigation and manipulation with the GenePalette software tool
Mark Rebeiz
University of Pittsburgh

2. CG13335 in situ Hybridization in fly embryos
Insert into pH-Stinger to see where expression is driven

4. What does GenePalette do?
Load genome sequences from any genome annotated in GenBank on any computer platform (Windows, Mac, Linux)
Design primers, search for motifs, look at restriction sites
Evolutionary comparisons of DNA conservation
Prepare “to scale” diagrams of gene structure for presentations and publication

5. Enter a query to GenBank
Select genes to work with from the
chromosomal region of interest

6. The region is loaded into a fully integrated interface, where every element is clickable/selectable

7. Search for motifs (restrictions sites, primers, transcription factor binding sites) within the loaded sequence to visualize where they occur

8. Design primers for PCR by simply selecting a region of DNA

9. Phylogenetic Footprinting
Regions that could be important for binding are often evolutionarily conserved

10. Phylogenetic footprinting is laborious by hand
Alignments of non-coding sequences are difficult, since there are lots of insertions/deletions (“indels”)
Often, binding sites are conserved, but not much else is
The methods for automating this process are clumsy

11. Sequence comparisons in GenePalette

13. GenePalette in the literature

14. Potential Projects Update the interface, make components easier to use
Automate the acquisition of orthologous sequences from databases
Improve accuracy and speed of algorithm for sequence alignment

15. Full text description
In the post-genomic era, the analysis of genomic sequence is a constant experimental need. A particularly challenging issue is determining the function of non-coding sequences that control when and where each gene is transcribed. Currently, a limited number of tools are available for aligning and visualizing regulatory sequence motifs in genomic DNA.The GenePalette software tool is a program written in the Rebeiz Lab at the University of Pittsburgh to handle this need. Coded in Java, this program allows users to download genome sequences from a database, and visualize features within the sequence using a graphical interface. 
Several independent improvements could be the focus of a capstone project: 
(1) Update the GUI to make it more user friendly. The software is used by many researchers (several thousand registered users) who are not necessarily computer savvy. Thus, improvements that facilitate logical use of components would greatly improve the software’s utility to researchers
(2) Streamline the acquisition of orthologous sequences from various databases. The software was originally designed to access GenBank, a fairly generic repository for DNA sequence data. However, several other extremely useful resources, such as ENSEMBL and UCSC are now available. In particular, the UCSC database contains a "concordance map” that allows users to find orthologous genomic sequences. This project would involve implementing an interface within the software to use these resources.
(3) Improve the sequence alignment algorithm. To compare and contrast evolutionary conservation or lack thereof, the software implements a sequence alignment algorithm that finds unique “words” of defined length that are identical between multiple sequences. These “landmarks” allow the user to assess whether individual motifs are conserved among species. The current algorithm is a slow “brute force” algorithm. This project would be to improve this algorithm to make it faster and more robust.