Hi Jim, Sorry for such a late response. I'm finally done with everything related to my orals, which went well.
It wasn't immediately clear to me how to read the base-pair sequence logo but I figured it out after reading the documentation. =) I like that when I hover over the base pair I can see the percentages of the different types of base pairs. Having two bases squeezed into one column makes it difficult for me to tell the difference between G and C, but I can always look at the sequence consensus to see which type of base pair I'm probably looking at. When there's quite a few different base pairs that occur in one position, it's hard to see what is occurring. Is there a way to export the percentages of the different types of base pairs? I work with non-canonical base pairs with the kink-turn sequence. GA base pairs actually stabilize the structure. I'd prefer if the base pairs that are displayed are based on the secondary structure specified, instead of just the canonical (and GU) base pairs. However, I can see that displaying all base pairs might be problematic. My advisor is showing Jan's version in his RNA bioinformatics class today. Do you think that output to a stockholm file would be possible? Cheers, Lauren On Mon, Sep 5, 2011 at 2:56 AM, Jim Procter <[email protected]> wrote: > > Hi Lauren ! Thanks for the nice comments :) > > On 05/09/2011 00:48, Lauren Lui wrote: >> >> I just took a look at what you did for the GSoC and it looks great! I >> might use it to help me make figures for my thesis proposal. > > great! A word of warning though : we still haven't got VARNA snapshots > stored within the Jalview project.. and VARNA snapshots from one version of > VARNA are not compatible with more recent versions, so you can't save any > annotated RNA diagrams at the moment. Yann Ponty is working on a new file > format for storing the VARNA display, but it won't be ready for a month or > two yet. >> >> It wasn't clear to me at first on how to access VARNA to look at the >> structure of the sequences, but I figured it out. Highlighting the >> nucleotide your mouse is hovering over in the alignment is very >> useful. > > it is ! (though you might notice a tiny bug in the highlighted position if > you are using a 'trimmed' model and there are gaps in the alignment) > >> Did the documentation for VARNA get put in the "Nucleic Acid >> Support" section? I couldn't find it in the webstart version. > > it actually is in the nucleic acids section - but there was a problem with > the automated build, so the version you used didn't include it. > > Happily, thanks to your email, I just fixed the issue, so you should be able > to see the help the next time you launch Jan's Jalview build. > > What do you think of the 'structure consensus' histogram and base-pair > sequence logo ? > > Jim. > > _______________________________________________ Jalview-dev mailing list [email protected] http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev
