UCSC Genome Browser new feature

주의 비디오 도움말: Multi-region visualization in the UCSC Genome Browser

This week’s video tip demonstrates a new feature at the UCSC 게놈 브라우저. I think it’s kind of unusual, and conceptually took me a little while to get used to when I started testing it. So I wanted to go over the basics for you, and give you a couple of tips on things that I had to grok as I got used to this new visualization option.

The headline for the news item describes it as: “Combine Multiple Regions of the Genome Browser into a Single Visualization!” 및

Have you ever wished you could remove all of the intronic or intergenic regions from the Genome Browser display? Have you ever dreamed of being able to visualize multiple far-flung regions of a genome? 음, now you can with the new “multi-region” option in the Genome Browser!

I should probably start with the first thing that confused me–the name “multi-region”. I thought that I was going to be able to see maybe part of a region on chromosome 1, and something on chromosome 8, maybe at the same time. But that’s not how this works. 이 경우에는, you look at multiple regions along the same chromosome, with some of the intervening sequences snipped out. This creates a sort of “virtual chromosome” for you to interact with.

이번 주 비디오, I’ll show you how that looks using the BRCA1 gene. First I show how you can look at all the exons together–with introns clipped out. And then I show how you can see the genes in the neighborhood displayed together, with the non-coding regions clipped out. 이들은 2 of the separate options for viewing.

내가 사용하는 “전망” menu option to illustrate this feature. But there is another way to access it–you can use the “multi-region” button in the browser buttons area.

multiregion_button

To keep the video short, I didn’t go into every detail on this tool. You should check out the news announcement for it, and the link to the additional details in the User Guide documentation 자세한. The new feature is also mentioned briefly in the lastest NAR paper on the UCSC Genome Browser (아래 링크). And you should try it out, 물론! That’s the best way to really understand how it might help you to visualize regions of the genome that you might be interested in.

Also as in the news, thanks to the development team. I am always looking for new visualizations, and this fun to test!

Thank you to Galt Barber, 마태 복음 Speir, and the entire UCSC Genome Browser quality assurance team for all of their efforts in creating these exciting new display modes.

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빠른 링크:

UCSC 게놈 브라우저: genome.ucsc.edu

News item on multi-region: http://genome.ucsc.edu/goldenPath/newsarch.html#030816

Training materials on the UCSC Genome Browser: http://openhelix.com/ucsc

참조:

박차, 엠, 분기, 대답 :, Rosenbloom, 사장님, 래니 소장, B를, 스폰서, B를, Nejad, 추신, 리, B를, 배운, 사장님, Karolchik, 디, 힌릭스, 대답 :, Heitner, 미국, 하트, 기철, Haeussler, 엠, Guruvadoo, 실은, 후지타, 추신, Eisenhart, C., Diekhans, 엠, 클로슨, 반장님, 캐스퍼, 제이, 이발사, 샷, Haussler, 디, Kuhn, 기철, & 켄트, 에. (2016). UCSC의 게놈 브라우저베이스: 2016 업데이트 핵산 연구, 44 (D1) 간접 자원부: 10.1093/nar/gkv1275

공개: UCSC Genome Browser tutorials are freely available because UCSC 스폰서 us to do training and outreach on the UCSC Genome Browser.