Comparative genome sequence navigation and manipulation with the GenePalette software tool

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Comparative genome sequence navigation and
manipulation with the GenePalette software tool
Mark Rebeiz University of Pittsburgh
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CG13335
in situ Hybridization in fly embryos
Insert into pH-Stinger to see where expression is
driven
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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

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Enter a query to GenBank
Select genes to work with from the chromosomal
region of interest
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The region is loaded into a fully integrated
interface, where every element is
clickable/selectable
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Search for motifs (restrictions sites, primers,
transcription factor binding sites) within the
loaded sequence to visualize where they occur
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Design primers for PCR by simply selecting a
region of DNA
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Phylogenetic Footprinting
Regions that could be important for binding are
often evolutionarily conserved
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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

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Sequence comparisons in GenePalette
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GenePalette in the literature
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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

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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 softwares 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.