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Topics - shuxiang

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Dear Xiangjun,

I used DSSR-enhanced visualization web server to display ribosome structures such as 5afi, 5j4b. All my tried failed. I'm not sure it is my browser problem or the web server inner error. Thank you.

Best,
Shuxiang   

2
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                                                           


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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.