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Questions and answers => RNA structures (DSSR) => Topic started by: shuxiang on May 15, 2018, 11:10:38 am

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Title: How to display RNA secondary structure with & in forna?
Post by: shuxiang 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                                                           

Title: Re: How to display RNA secondary structure with & in forna?
Post by: xiangjun 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
Title: Re: How to display RNA secondary structure with & in forna?
Post by: shuxiang on May 15, 2018, 11:35:00 am
It works. Thank you so much. :)

Created and maintained by Dr. Xiang-Jun Lu [律祥俊], Principal Investigator of the NIH grant R01GM096889
Dr. Lu is currently affiliated with the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.