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1. Datasets Here are links to the two datasets of compared fragments. Each row is in format: fragment-num pdbId from to Note that the fields from and to indicated the serial index of the C-alpha from the beginning of the pdb file, and NOT residue indices as given by the PDB file. 2_SH.txt 8_SH.txt |
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2. GOSSIP output file Here is a link to the result files produced by gossip under parameter values: Similarity Threshold=0.8, Accuracy Threshold=2.0. Each row is in format: frag-num1 frag-num2 alignment-size transformation 2_SH_GOSSIP.comp 8_SH_GOSSIP.comp |
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3. MultiProt output file Here is a link to the result files produced by MultiProt under parameter value: Accuracy Threshold=2.0. Since MultiProt is a local alignment program, these files also contains result of matching pairs with less than 80% similarity. Each row is in format: frag-num1 frag-num2 frag1-size frag2-size alignment-size 2_SH_MultiProt.comp 8_SH_MultiProt.comp |
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4. YAKUSA output files Here is a link to the result files extracted from YAKUSA output: YAKUSA was run with default parameters, except for changing minimal seed length to 4 (default 6), and maximal result number to 500 (default 50). Since YAKUSA is a local alignment program, these files also contains result of matching pairs with less than 80% similarity. Each row is in format: frag-num1 frag-num2 frag1-size frag2-size alignment-size 2_SH_YAKUSA.comp 8_SH_YAKUSA.comp |
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5. Statistical Analysis files The following files contain the statistical analysis of the results produced by the three methods The files contain a list of unique similarities identified by each method, a list of similarities missed by only one of the methods, and general statistics. 2_SH_analysis.txt 8_SH_analysis.txt |