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Describe your research and the big picture problem or puzzle it addresses.

You probably hear about “new” genomes being sequenced all the time now. The DNA sequences of so many species have become available lately, it’s hard to keep up. And traditional publication methods don’t really help you to explore all that sequence information.

What did you do?

We worked with the UCSC Genome Browser folks to help people examine the DNA sequences from the genome projects, as well as how to visualize and explore many other data types that you need to provide additional context for the genome regions that people are interested in.

What did you find?

There are a lot of different ways to represent the features that people need to know about–genes, the small changes that we call SNPs or simple nucleotide polymorphisms, the promoter regions that help genes to be turned on or off, and how similar or different sequences are across other species’ genomes. We show people how these look, and how they can use the software tool to display the key things that they need. And we show them how to query the database to make new discoveries in the data.

Describe the limitations.

The way we show single linear genomes today is helpful and necessary, but increasingly we are going to need new strategies to look at the similarities and differences of many genomes that are all lined up together. We’ll need new strategies to explore and query them as well.

What are the takeaways?

Software tools for exploring genome sequences are crucial for science today, and it’s important to understand how the features look and line up. Using these tools effectively and efficiently will help researchers to plan new experiments and evaluate new data that they generate.

Mangan, M. E., Williams, J. M., Kuhn, R. M., & Lathe, W. C. (2014). The UCSC genome browser: what every molecular biologist should know. Current Protocols in Molecular Biology, 19-9.

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