Question about genome versions in Multiz alignment

Sharp, Sandra

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Jul 11, 2024, 3:02:43 PMJul 11

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Dear Genome Team:

I would like to find the location of a conserved sequence in mouse and pig using the Multiz alignment information. I am working in mm10. The location given at the "B" link for pig is in genome version Sscrofa10.2/susScr3. Is there a way to get the location in pig genome Sscrofa 11.1short of doing another Short Sequence Match in the 11.1 genome?

Many thanks,

Sandy

Sandra B. Sharp, Ph.D.

Professor emerita, Biological Sciences, CalStateLA

Sharp, Sandra

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Jul 15, 2024, 3:56:38 PM (10 days ago) Jul 15

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Never mind - I found the information for liftover and Convert. I knew I'd seen it somewhere and finally landed on the right search terms. Great tools! Thank you!

Sandy Sharp

From: Sharp, Sandra
Sent: Thursday, July 11, 2024 12:01 PM
To: gen...@soe.ucsc.edu <gen...@soe.ucsc.edu>
Subject: Question about genome versions in Multiz alignment

Sharp, Sandra

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Jul 15, 2024, 3:56:40 PM (10 days ago) Jul 15

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This just occurred to me. Is there a way for the user to choose which assembly is used in the Multiz alignment? For example, is it possible to change the pig build being used in the Multiz alignment from SGSC Sscrofa10.2/susScr3 to Sscrofa11.1/susScr11? If there is, it would make it easier than using liftover, convert, or Short sequence match for what I'm doing. Thanks.

Sandy Sharp

From: Sharp, Sandra <ssh...@exchange.calstatela.edu>
Sent: Saturday, July 13, 2024 11:22 AM
To: gen...@soe.ucsc.edu <gen...@soe.ucsc.edu>
Subject: Re: UPDATE: Question about genome versions in Multiz alignment

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