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How do I switch between viewing the negative strand and positive strand in a sequence?

asked 2015-12-29 03:32:17 -0700

Whit Athey gravatar image

I am using GH version for Win 7 (64) downloaded Dec 2015

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answered 2015-12-30 15:03:53 -0700

Hi Whit,

Are you looking at a reference sequence file or a gene annotation file? Both forward and reverse strand information is available for any reference sequence plot just by increasing the vertical height of the graph. It would look something like the below figure, where the top information is for the forward strand and the bottom information is the reverse strand at this location.

image description

If you are looking at a gene annotation file then the strand for a gene is fixed based on strand field listed in the source of the annotation information.

image description

Any gene listed on the forward strand will be colored blue and any gene on the reverse strand will be green.

Let me know if you have any further questions.

Thanks, Jami...

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I am new at this, obviously, but now I see that in the reference pane I have a transcript from some publication that happened to sequence the reverse strand. That undoubtedly forced the view of my own sequence in the top pane to also be the reverse (negative) strand.

Whit Athey ( 2015-12-30 17:12:34 -0700 )edit

I am not interested in comparing to some particular transcript, but rather to the consensus reference (forward) sequence. How can I force the browser to use this reference? I have already selected HUGO v 105 in the upper left pane--isn't that what I want?

Whit Athey ( 2015-12-30 17:14:28 -0700 )edit

Hi Whit, I am not entirely sure about what you are seeing in your GenomeBrowse view. Can you provide a screenshot on the site here or email it to support@goldenhelix.com and I can take a look to see how we can help. Thanks, Jami...

Jami Bartole ( 2015-12-31 08:56:51 -0700 )edit
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Asked: 2015-12-29 03:32:17 -0700

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Last updated: Dec 30 '15