loops into lines

3 replies [Last post]
pgn
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Joined: 02/19/2011

Hi. I would like to ask how to make this marked circular structure from the picture flat/linear? because I'm interested only in created hairpins and loop makes this picture unclear.

http://img404.imageshack.us/img404/8387/58134316.jpg

zukerm
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Joined: 11/12/2010
Drawing secondary structures.

Your comment is unclear, so I'll guess what you mean. I think that you do not like the large loop that you circled in red. You cannot make the structure "flat/linear". You must create a new structure that does not have this loop.

I refolded your sequence setting the maxbp parameter to 100. That means that predicted structures will not contain base pairs between nucleotides more than 100 apart in the sequence. The result is displayed on the right. Is this what you want? .

admin
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Joined: 09/23/2010
I've inserted the image for

I've inserted the image for easier access. Click for a larger view.

amanmann
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Joined: 04/01/2011
Flat structure

I want to obtain a secondary structure of a single stranded DNA sequence. I would like to get ride of the exterior loop. The flat option mentioned above by Dr. Zuker is not visible on the mfold page to fold DNA. I looked at the primary results page also but did not find any link to other ways of displaying the structure. How do I get the flat structure.
Thanks