Does RNA parses checkpoint matrix as well as protein

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    • March 5, 2014 at 2:03 pm #1846
      Anonymous

        Hi,

        I am recently studying Rosetta for rna prediction.

        When Rosetta make fragments for proteins, there are a step to prase a PSI-BLAST binary checkpoint file. The output likes as follows:
        G 0.0783 0.0108 0.0337 0.0256 0.0162 0.5101 0.0135 0.0189 0.0337 0.0283 0.0094 0.0391 0.0189 0.0189 0.0229 0.0513 0.0297 0.0243 0.0054 0.0108
        S 0.1099 0.0175 0.0489 0.0524 0.0209 0.0663 0.0192 0.0297 0.0541 0.0419 0.0157 0.0541 0.0297 0.0332 0.0401 0.2199 0.0820 0.0419 0.0052 0.0175
        G 0.0783 0.0108 0.0337 0.0256 0.0162 0.5101 0.0135 0.0189 0.0337 0.0283 0.0094 0.0391 0.0189 0.0189 0.0229 0.0513 0.0297 0.0243 0.0054 0.0108
        M 0.0522 0.0161 0.0201 0.0281 0.0482 0.0281 0.0161 0.1004 0.0361 0.1968 0.1606 0.0201 0.0161 0.0281 0.0321 0.0361 0.0402 0.0924 0.0080 0.0241
        K 0.0570 0.0086 0.0415 0.0708 0.0155 0.0432 0.0207 0.0276 0.2781 0.0432 0.0155 0.0415 0.0276 0.0535 0.1071 0.0535 0.0397 0.0328 0.0052 0.0173
        E 0.0552 0.0074 0.0902 0.2965 0.0166 0.0350 0.0258 0.0221 0.0755 0.0368 0.0129 0.0405 0.0258 0.0645 0.0497 0.0552 0.0368 0.0313 0.0055 0.0166
        F 0.0448 0.0116 0.0155 0.0229 0.0984 0.0218 0.0096 0.0794 0.0236 0.2947 0.0403 0.0143 0.0184 0.0191 0.0234 0.0307 0.0365 0.0773 0.0097 0.0356

        So I wonder how I can get this profile ( parsing checkpoint matrix ) for RNA. Does Rosetta have this tools or codes? Yet without it, would you please give me some other methods to accomplish the same goal.

        Thank you very much!

      • March 5, 2014 at 3:05 pm #9859
        Anonymous

          The RNA applications make use of a different fragment generation scheme than does the protein prediction algorithms. (RNA structure has much less local sequence dependance than protein does, so PSSMs are less useful to use with structural predictions.) See https://www.rosettacommons.org/manuals/archive/rosetta3.5_user_guide/d2/d82/rna_denovo.html for how to do abinitio with RNA structures. This includes a description of the rna_database application, which is the program used to make the fragment libraries for RNA – note that it does not need a PSSM or PSI-BLAST checkpoint file to work.

          Besides ab inito, the other main place where fragments are used is in loop modeling. Again, RNA has its own way of doing loop modeling. See https://www.rosettacommons.org/manuals/archive/rosetta3.5_user_guide/d3/d28/swa_rna_loop.html for details.

        • March 7, 2014 at 6:20 am #9865
          Anonymous

            Thank you for your help.

            There are further question to ask. Taking protein as an example. When Blast produced a binary checkpoint_file, Rosetta changed this binary checkpoint file into probability like the form of first floor by a function @checkpoint_matrix = &parse_checkpoint_file(“$id$chain.nr.chk”) in make_fragments.pl;

            1) So I would like to know what’s the meaning of this checkpoint, and what is the different from PSSM also produced by blast -Q.
            2) How can I get the probability from checkpoint file for RNA by Rosetta or other methods. Without the tools, would you tell me what’s the theory which I can get it.

            I am sorry for my naive and inarticulate questions. Thank you again!

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