question about batch search for Multiz Alignment

[Lo, Chiao-Ling]

Hi, 

I am wondering if it possible to do batch search in Multiz Alignment. For example, I have a list of rat positions that I want to find the corresponding chromosome location in human of the aligned positions. Can I get this information through Mutiz Alignment? 

Thank you, 

Sherry

Chiao-Ling Lo (Sherry), PhD 

Research Associate 

Department of Anatomy & Cell Biology ​

Indiana University School of Medicine 

1044 W. Walnut St, R4 W041

Indianapolis, IN 46202

765-586-7804

[Matthew Speir]

Hi Chiao-Ling,

Thank you for your question about finding corresponding rat regions in the human genome.

I would recommend using the "LiftOver" tool: http://genome.ucsc.edu/cgi-bin/hgLiftOver. Select the rat assembly you're working with as your "original assembly" and then select the human assembly that you're interested in as your "new assembly". Then paste your regions into the box below and click "submit", after the page refreshes, you should see a link to download your results.

I would recommend using at least BED4 format: http://genome.ucsc.edu/FAQ/FAQformat.html#format1, which includes a name column so that you can link your input regions with your output regions.

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Matthew Speir
UCSC Genome Bioinformatics Group

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