ClaRNA_play ------------------------------------------------------------------------------- Author: @wkdawson based on the code and publication of T. Waleń, G. Chojnowski, P. Gierski, and J. M. Bujnicki, “ClaRNA: a classifier of contacts in RNA 3D structures based on a comparative analysis of various classification schemes.,” Nucleic Acids Research, vol. 42, no. 19, pp. e151–e151, Oct. 2014. Integrate/tested by @mmagnus # Install pip install rna-tools simplejson networkx==1.8.1 scipy # tested with simplejson==3.17.0 # Start To start: $ rna_clarna_run.py -ipdb test_data/3e5fA_M15_c.pdb > test_output/3e5fA_M15_c.pdb.outCR $ rna_clarna_run.py -ipdb test_data/3e5fA_M500_c.pdb > test_output/3e5fA_M500_c.pdb.outCR to analyze: $ rna_clarna_compare.py -iref test_output/3e5fA_M15_c.pdb.outCR -ichk test_output/3e5fA_M500_c.pdb.outCR 3e5A_M15_c.pdb.outCR 3e5fA_M500_c.pdb.outCR 0.662 NA 0.647 0.707 0.538 0.778 0.500 1.000 ![](docs/clarna_run.png) Tested with ClaRNA only. $ rna_clarna_run.py -ipdb test_data/3e5fA_M500_c.pdb Classifier: Clarna A 5 A 49 bp C G WW_cis 0.6965 A 6 A 48 bp C G WW_cis 0.6878 A 10 A 34 bp A U WW_cis 0.6209 A 10 A 35 bp A U WW_cis 0.6951 A 13 A 28 bp A G WW_cis 0.9170 A 14 A 27 bp U A WW_cis 0.7730 A 15 A 26 bp G C WW_cis 0.8426 A 16 A 25 bp G C WW_tran 0.6505 A 17 A 24 bp C G WW_cis 0.7311 A 18 A 23 bp G C WW_tran 0.7475 A 31 A 36 bp G G HW_tran 0.6888 A 41 A 46 bp C G WW_cis 0.8555 ## Get secondary structure First, you have to make a binary file of Michal's program. Go to `lib/ClaRNAwd_to_vienaSS/` and run `make` you should get a binary file. Now you can run: $ lib/ClaRNAwd_to_vienaSS/ClaRNAwd_output_parser_get_SS test_output/3e5fA_M15_c.pdb.outCR (((((..(((...(((......)))......)))....((....))))))). or $ lib/ClaRNAwd_to_vienaSS/ClaRNAwd_output_parser_get_SS lib/ClaRNAwd_to_vienaSS/example.pdb.outCR (((((......)))))........(.((....(.......)..(((. .)))...)).) .....((((((......................))))))........ ........... To "re-make" the installation do `make clean` and `make` again. ## Compare two structures .. `rna_clarna_compare.py -v`: $ rna_clarna_compare.py -v -iref test_output/3e5fA_M15_c.pdb.outCR -ichk test_output/3e5fA_M500_c.pdb.outCR test_output/3e5fA_M15_c.pdb.outCR test_output/3e5fA_M15_c.pdb.outCR A 2 A 52 bp U A WW_cis 0.9511 A 3 A 51 bp U A WW_cis 0.8414 A 4 A 50 bp C G WW_cis 0.7113 A 5 A 49 bp C G WW_cis 0.9349 A 6 A 48 bp C G WW_cis 0.8963 A 9 A 35 bp A U WW_cis 0.7912 A 10 A 34 bp A U WW_cis 0.9165 A 11 A 33 bp G C WW_cis 0.8996 A 13 A 27 bp A A WW_tran 0.6134 A 13 A 28 bp A G WW_cis 0.8797 A 15 A 26 bp G C WW_cis 0.8868 A 16 A 25 bp G C WW_cis 0.7712 A 17 A 24 bp C G WW_cis 0.9009 A 18 A 23 bp G C WW_tran 0.7947 A 19 A 22 bp G A SH_tran 0.7556 A 31 A 36 bp G G HW_tran 0.8840 A 38 A 48 bp A G WS_tran 0.6725 A 40 A 47 bp C G WW_cis 0.9030 A 41 A 46 bp C G WW_cis 0.8988 test_output/3e5fA_M500_c.pdb.outCR A 5 A 49 bp C G WW_cis 0.6965 A 6 A 48 bp C G WW_cis 0.6878 A 10 A 34 bp A U WW_cis 0.6209 A 10 A 35 bp A U WW_cis 0.6951 A 13 A 28 bp A G WW_cis 0.9170 A 14 A 27 bp U A WW_cis 0.7730 A 15 A 26 bp G C WW_cis 0.8426 A 16 A 25 bp G C WW_tran 0.6505 A 17 A 24 bp C G WW_cis 0.7311 A 18 A 23 bp G C WW_tran 0.7475 A 31 A 36 bp G G HW_tran 0.6888 A 41 A 46 bp C G WW_cis 0.8555 compare: 3e5fA_M15_c.pdb.outCR 3e5fA_M500_c.pdb.outCR reference vs prediction: WC ref 13 pred-match 7 nWC ref 6 pred-match 3 stack ref 0 pred-match 0 prediction vs reference: WC pred 8 ref-match 6 nWC pred 4 ref-match 4 stack pred 0 ref-match 0 for all motifs:nref 19, nchkTP 10, nFN 9 nchk 12, nrefTP 10, nFP 2 summary: inf_all 0.662 inf_stack -999.999 inf_WC 0.647 inf_nWC 0.707 SNS_WC 0.538 PPV_WC 0.778 SNS_nWC 0.500 PPV_nWC 1.000 ## Example with two chains $ rna_clarna_run.py -ipdb test_data/5k7c_clean_onechain_renumber_as_puzzle_srr_AB.pdb Classifier: Clarna # A:1-47 B:52-62 A 1 A 16 bp C G WW_cis 0.8667 A 2 A 15 bp G C WW_cis 0.9263 A 3 A 14 bp U A WW_cis 0.9244 A 4 A 20 bp G A SH_cis 0.6670 A 4 A 13 bp G C WW_cis 0.9239 A 4 A 21 bp G A SW_tran 0.7298 A 5 A 24 bp G G SS_tran 0.7785 A 5 A 12 bp G C WW_cis 0.8932 A 6 A 39 bp U A WW_cis 0.8611 A 7 A 38 bp U A WW_cis 0.9304 A 8 A 37 bp A U WW_cis 0.9297 A 9 A 36 bp G C WW_cis 0.9159 A 10 A 35 bp G C WW_cis 0.9070 A 11 A 34 bp G C WW_cis 0.9215 A 14 A 20 bp A A SW_cis 0.6638 A 15 A 19 bp C A SW_cis 0.7975 A 16 A 17 bp G U SW_cis 0.6665 A 25 B 62 bp U A WW_cis 0.8659 A 27 B 60 bp G C WW_cis 0.7851 A 28 B 59 bp C G WW_cis 0.8167 A 29 B 58 bp U U WW_cis 0.8238 A 33 A 41 bp G C WW_cis 0.9406 A 40 A 41 bp G C SH_cis 0.6214 A 42 B 57 bp G G HS_tran 0.7572 A 44 B 55 bp U A WW_cis 0.8551 A 45 B 54 bp G C WW_cis 0.8454 A 46 B 53 bp A U WW_cis 0.8995 # Warning I changed the default value -9999 to 0. I don't know it this simplification is good in your projects! Think about it!