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Author Topic: How to display RNA secondary structure with & in forna?  (Read 22883 times)

Offline shuxiang

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How to display RNA secondary structure with & in forna?
« on: May 15, 2018, 11:10:38 am »
Dear Xiangjun,

I tried to use the following dbn file generated by DSSR and display its RNA secondary structure in forna (a RNA secondary structure visualization tool). However, it looks like forna doesn't recognize multiple sequences and "&" notation. It there a way to get around this? Thank you.

>2F4V nts=1511 [2F4V] -- secondary structure derived by DSSR
UGGAGAGUUUGAUCCUGGCUCAGGGUGAACGCUGGCGGCGUGCCUAAGACAUGCAAGUCGUGCGGG&CCGCGGGGUUUU&ACUCCG&UGGUC&AGCGGCGGACGGGUGAGUAACGCGUGGGUGACCUACCCGGAAGAGGGGGACAACCCGGGGAAACUCGGGCUAAUCCCCCAUGUGGACCCGCCCCUUGGGGUGUGUCCAAAGGGCUUU&GCCCGCUUCCGGAUGGGCCCGCGUCCCAUCAGCUAGUUGGUGGGGUAAUGGCCCACCAAGGCGACGACGGGUAGCCGGUCUGAGAGGAUGGCCGGCCACAGGGGCACUGAGACACGGGCCCCACUCCUACGGGAGGCAGCAGUUAGGAAUCUUCCGCAAUGGGCGCAAGCCUGACGGAGCGACGCCGCUUGGAGGAAGAAGCCCUUCGGGGUGUAAACUCCUGAA&CCCGGGACGAAACCCCCGACGA&GGGGACUGACGGUACCGGG&GUAAUAGCGCCGGCCAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGGCGCGAGCGUUACCCGGAUUCACUGGGCGUAAAGGGCGUGUAGGCGGCCUGGGGCGUCCCAUGUGAAAGACCACGGCUCAACCGUGGGGGAGCGUGGGAUACGCUCAGGCUAGACGGUGGGAGAGGGUGGUGGAAUUCCCGGAGUAGCGGUGAAAUGCGCAGAUACCGGGAGGAACGCCGAUGGCGAAGGCAGCCACCUGGUCCACCCGUGACGCUGAGGCGCGAAAGCGUGGGGAGCAAACCGGAUUAGAUACCCGGGUAGUCCACGCCCUAAACGAUGCGCGCUAGGUCUCUGGGUCU&CCUGGGGGCCGAAGCUAACGCGUUAAGCGCGCCGCCUGGGGAGUACGGCCGCAAGGCUGAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAAGCAACGCGAAGAACCUUACCAGGCCUUGACAUGCUAGGGAACCCGGGUGAAAGCCUGGGGUGCCCCGCGAGGGGAGCCCUAGCACAGGUGCUGCAUGGCCGUCGUCAGCUCGUGCCGUGAGGUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCCCGCCGUUAGUUGCCAGCGGUUCGGCCGGGCACUCUAACGGGACUGCCCGCGAAAGCGGGAGGAAGGAGGGGACGACGUCUGGUCAGCAUGGCCCUUACGGCCUGGGCGACACACGUGCUACAAUGCCCACUACAAAGCGAUGCCACCCGGCAACGGGGAGCUAAUCGCAAAAAGGUGGGCCCAGUUCGGAUUGGGGUCUGCAACCCGACCCCAUGAAGCCGGAAUCGCUAGUAAUCGCGGAUCAGCCAUGCCGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACGCCAUGGGAGCGGGCUCUACCCGAAGUCGCCGGG&AGCCUACGGG&CAGGCGCCGAGGGUAGGGCCCGUGACUGGGGCGAAGUCGUAACAAGGUAGCUGUACCGGAAGGUGCGGCUGGAUC&A&UUCU
....((((..[.[[[..)))).((((.(((((..(((((((((....(((.(((..(((..((.((&((((((((....&.)))))&)))))&.)))))......(((......((((((((..((...(((((((.(((((....((((((....)))))).....)))))....((((.(((((....))))).))))...((((...&)))).)))))))..))))))))))(((....(((..((((((((.......)))))))))))......)))..((((((((....))))...))))))).(((((............))))).((((....))))...)))))).).....(.(((...((.((....)).).))))).)).))))))..((((.......(((....)))......))))....&(.(((...(....((((.....&)))).....)....))).)&......((((([[[...(((((.....((.]]])).......))))))))))..)))))))))..........((([[...(.((((...(((.(((((((.((((((((((......((((((.....))))))....))))))))..)))))))))..(((.(((((...((((((((...(((((((....((........)).......)))))))...).......((....)).)))))))..)))))..))..))))...))))....((((((...((...((((.........))))...))))))))......{...((((((..((((((((((...&))))))))))...((..]])).....)))))))))).(((......((((....))))....)))...]]].](((((.(((((((.((..(((((..((((((((((......((........))..........((((((...(...((............(.(....).)........(((....).))........))).((.(((...((((((.(....(((((((((....)))..((((......))))..)))))).....((((.(((((.....(....(.......)..)......)))))..(..(((((....))))).....)..)))).....).).)))...)).))))).....))))))..[)).)))))))).(...(((((((.....(((..((..((((....))))..))....))).....)))))))......(....(((((((........)))))))....)..)..))))).....(((((((......]...)))))))......))...)))))))))).))..(.(..((.(.((((.(((..((.(((.((((((...(.((((...&.(((....))&).)))).)..)))))).))).))..))).))))..).))...)..)..(((((((((....)))))))))}....&.&....

Best,
Shuxiang                                                           


Offline xiangjun

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Re: How to display RNA secondary structure with & in forna?
« Reply #1 on: May 15, 2018, 11:23:34 am »
Hi Shuxiang,

The '&' symbol in DSSR-derived dot-bracket-notation (DBN) is a convention between DSSR and VARNA to signify different chains or breaks between different segments of the same chain. Other 2D viewers may not recognize it, as is the case for FORNA.

You could use the --dbn-break=no option to remove them, as documented in the DSSR manual (Section 3.16.12, shown below).

3.16.12 The --dbn-break option

By default, DSSR employs the symbol ‘&’ to separate multiple chains or
chain breaks in dbn, for compatibility with VARNA. By using
--dbn-break, one can choose any of the characters in the string
“&.:,|+”. For example, by running the following command on the
Dickerson DNA dodecamer [16] structure 355d, one would get a
whole-structure dbn composed of those from the two chains
connected by ‘+’:

------------------------------------------------------------
x3dna-dssr --dbn-break=+ -i=355d.pdb

>355d nts=24 [whole]
CGCGAATTCGCG+CGCGAATTCGCG
((((((((((((+))))))))))))
------------------------------------------------------------

With --dbn-break=no, no symbol will be used to separate different
chains or intra-chain breaks: for 355d, the dbn would be
(((((((((((()))))))))))).

HTH,

Xiang-Jun
« Last Edit: May 15, 2018, 11:25:25 am by xiangjun »

Offline shuxiang

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Re: How to display RNA secondary structure with & in forna?
« Reply #2 on: May 15, 2018, 11:35:00 am »
It works. Thank you so much. :)

 

Funded by the NIH R24GM153869 grant on X3DNA-DSSR, an NIGMS National Resource for Structural Bioinformatics of Nucleic Acids

Created and maintained by Dr. Xiang-Jun Lu, Department of Biological Sciences, Columbia University