Timeline for Finding RNA Loops
Current License: CC BY-SA 3.0
12 events
| when toggle format | what | by | license | comment | |
|---|---|---|---|---|---|
| Dec 11, 2013 at 2:56 | comment | added | bobthejoe | As an improvement to what @WYSIWYG mentioned, PARS is fairly low resolution since it is still enzyme based. The newer in vivo SHAPE or DMS-seq methods are much better and more informative. | |
| Dec 10, 2013 at 22:25 | answer | added | bobthejoe | timeline score: 2 | |
| Dec 6, 2013 at 18:48 | comment | added | shigeta | any reviews? the last time i looked this was not a completely solved problem. | |
| Dec 6, 2013 at 14:16 | comment | added | WYSIWYG | EDIT: Anything flanked by a half-stem (which pair with each other) should be a loop | |
| Dec 6, 2013 at 11:23 | comment | added | WYSIWYG | Recently sequencing approach has been extended to obtain RNA secondary structures in-vivo by using a soluble RNA-methylating agent (DMS). | |
| Dec 6, 2013 at 11:21 | comment | added | WYSIWYG | as @MadScientist said mfold or RNAfold(Vienna) should work for secondary structure prediction. Anything flanked by a half-stem should be a loop. Both mfold and RNAfold have a limit on the size of the sequence. They don't take large sequences and splitting the sequence is not a great option because the local MFE may be different from the global one. There is also an experimental technique called PARS in which the RNA is digested with different RNAses (V1, S1) and base-paired regions are identified by sequencing | |
| Dec 5, 2013 at 6:08 | comment | added | shigeta | just looking for helices. i wasn't aware that was trivial.. is mfold accurate? | |
| Dec 4, 2013 at 10:43 | history | tweeted | twitter.com/#!/StackBiology/status/408184739305390080 | ||
| Dec 4, 2013 at 6:30 | comment | added | Mad Scientist | So you only need to find the helices, from there identifying the loops is trivial. Can the loops have interactions with other parts of the RNA, e.g. pseudoknots? If not, any secondary structure prediction program like mfold should suit your purpose. | |
| Dec 4, 2013 at 6:03 | comment | added | shigeta | A loop in this case would be the result of an RNA helix from a single stranded RNA. The loop would be the result of the strand forming a helix by itself. | |
| Dec 3, 2013 at 21:00 | comment | added | Mad Scientist | What exactly do you mean by loops? Just unstructured parts of the RNA (= not in any base pairs)? | |
| Dec 3, 2013 at 20:41 | history | asked | shigeta | CC BY-SA 3.0 |