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RNAcentral / r2dt-web

Web component for visualising RNA secondary structure in standard orientations
https://rnacentral.github.io/r2dt-web/
Apache License 2.0
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my seq did not match selected template #6

Open FCo2GNT opened 2 years ago

FCo2GNT commented 2 years ago

Hi, I would like to visualize the 2ndary structure of a RNA sequence , based on a U7snRNA template (mus musculus). But this is not working with the current setup of the tool. do you have any advice?

AntonPetrov commented 2 years ago

Hi @FCo2GNT!

Thank you for reaching out! If you are okay with sharing the sequence that did not work here or by email, I can debug this and try to generate a diagram. If the sequence is private, my guess would be that it could contain large insertions that confuse R2DT, but without looking at a specific case, it's hard to tell.

FCo2GNT commented 2 years ago

Thank you very much for your answer, unfortunately I cannot share with you this sequence. My seq is 443bp , so there are no large insertions compared to the original U7 snRNA structure, but probably the modifications that we made are enough to confuse the tool… I will try to see if I can overcome this, Again, thank you

From: Anton Petrov @.> Sent: jeudi 17 février 2022 12:37 To: RNAcentral/r2dt-web @.> Cc: Fanny COLLAUD @.>; Mention @.> Subject: Re: [RNAcentral/r2dt-web] my seq did not match selected template (Issue #6)

Hi @FCo2GNThttps://github.com/FCo2GNT!

Thank you for reaching out! If you are okay with sharing the sequence that did not work here or by emailhttps://www.ebi.ac.uk/about/people/anton-petrov, I can debug this and try to generate a diagram. If the sequence is private, my guess would be that it could contain large insertions that confuse R2DT, but without looking at a specific case, it's hard to tell.

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AntonPetrov commented 2 years ago

Of course, I understand.

For U7 snRNA, R2DT uses the RF00066 Rfam family as a template, which is much smaller than 443 bps (in human, U7 is only 63 nucleotides, for example). This is the most likely explanation for the problem.