├── LICENSE.TXT ├── README.TXT ├── README_IMK.md ├── db ├── db.tsv └── params │ ├── D00001.001.txt │ ├── D00001.004.txt │ ├── D00002.001.txt │ ├── D00003.001.txt │ ├── D00004.001.txt │ ├── D00005.001.txt │ ├── D00006.001.txt │ ├── D00007.001.txt │ ├── D00008.001.txt │ ├── D00009.001.txt │ ├── D00010.001.txt │ ├── D00011.001.txt │ ├── D00013.001.txt │ ├── D00014.001.txt │ ├── D00015.001.txt │ ├── D00016.001.txt │ ├── D00017.001.txt │ ├── D00018.001.txt │ ├── D00019.001.txt │ ├── D00020.001.txt │ ├── D00021.001.txt │ ├── D00021.005.txt │ ├── D00022.001.txt │ ├── D00022.002.txt │ ├── D00023.001.txt │ ├── D00024.001.txt │ ├── D00024.004.txt │ ├── D00025.001.txt │ ├── D00026.001.txt │ ├── D00027.001.txt │ ├── D00027.003.txt │ ├── D00028.001.txt │ ├── D00028.002.txt │ ├── D00029.001.txt │ ├── D00030.001.txt │ ├── D00030.004.txt │ ├── D00031.001.txt │ ├── D00032.001.txt │ ├── D00033.001.txt │ ├── D00034.001.txt │ ├── D00035.001.txt │ ├── D00036.001.txt │ ├── D00037.001.txt │ ├── D00037.003.txt │ ├── D00038.001.txt │ ├── D00038.003.txt │ ├── D00039.001.txt │ ├── D00040.001.txt │ ├── D00040.003.txt │ ├── D00041.001.txt │ ├── D00042.001.txt │ ├── D00043.001.txt │ ├── D00044.001.txt │ ├── D00045.001.txt │ ├── D00046.001.txt │ ├── D00047.001.txt │ ├── D00048.001.txt │ ├── D00049.001.txt │ ├── D00050.001.txt │ ├── D00051.001.txt │ ├── D00052.001.txt │ ├── D00052.002.txt │ ├── D00052.003.txt │ ├── D00053.001.txt │ ├── D00054.001.txt │ ├── D00055.001.txt │ ├── D00055.004.txt │ ├── D00056.001.txt │ ├── D00057.001.txt │ ├── D00058.001.txt │ ├── D00058.004.txt │ ├── D00059.001.txt │ ├── D00060.001.txt │ ├── D00061.001.txt │ ├── D00062.001.txt │ ├── D00062.004.txt │ ├── D00063.001.txt │ ├── D00064.001.txt │ ├── D00065.001.txt │ ├── D00066.001.txt │ ├── D00067.001.txt │ ├── D00067.004.txt │ ├── D00068.001.txt │ ├── D00069.001.txt │ ├── D00070.001.txt │ ├── D00071.001.txt │ ├── D00071.003.txt │ ├── D00072.001.txt │ ├── D00073.001.txt │ ├── D00074.001.txt │ ├── D00075.001.txt │ ├── D00076.001.txt │ ├── D00077.001.txt │ ├── D00078.001.txt │ ├── D00079.001.txt │ ├── D00080.001.txt │ ├── D00081.001.txt │ ├── D00082.001.txt │ ├── D00083.001.txt │ ├── D00084.001.txt │ ├── D00085.001.txt │ ├── D00086.001.txt │ ├── D00086.002.txt │ ├── D00086.003.txt │ ├── D00087.001.txt │ ├── D00088.001.txt │ ├── D00089.001.txt │ ├── D00090.001.txt │ ├── D00091.001.txt │ ├── D00092.001.txt │ ├── D00093.001.txt │ ├── D00094.001.txt │ ├── D00095.001.txt │ ├── D00096.001.txt │ ├── D00097.001.txt │ ├── D00098.001.txt │ ├── D00099.001.txt │ ├── D00100.001.txt │ ├── D00101.001.txt │ ├── D00102.001.txt │ ├── D00102.002.txt │ ├── D00102.003.txt │ ├── D00102.004.txt │ ├── D00103.001.txt │ ├── D00104.001.txt │ ├── D00105.001.txt │ ├── D00106.001.txt │ ├── D00107.001.txt │ ├── D00108.001.txt │ ├── D00109.001.txt │ ├── D00110.001.txt │ ├── D00110.002.txt │ ├── D00111.001.txt │ ├── D00111.002.txt │ ├── D00112.001.txt │ ├── D00113.001.txt │ ├── D00114.001.txt │ ├── D00114.002.txt │ ├── D00114.003.txt │ ├── D00114.004.txt │ ├── D00114.005.txt │ ├── D00115.001.txt │ ├── D00116.001.txt │ ├── D00117.001.txt │ ├── D00117.002.txt │ ├── D00117.003.txt │ ├── D00118.001.txt │ ├── D00118.002.txt │ ├── D00119.001.txt │ ├── D00120.001.txt │ ├── D00121.001.txt │ ├── D00122.001.txt │ ├── D00122.002.txt │ ├── D00122.003.txt │ ├── D00123.001.txt │ ├── D00123.002.txt │ ├── D00124.001.txt │ ├── D00125.001.txt │ ├── D00126.001.txt │ ├── D00127.001.txt │ ├── D00128.001.txt │ ├── D00128.002.txt │ ├── D00128.003.txt │ ├── D00128.004.txt │ ├── D00128.005.txt │ ├── D00128.006.txt │ ├── D00129.001.txt │ ├── D00130.001.txt │ ├── D00131.001.txt │ ├── D00132.001.txt │ ├── D00133.001.txt │ ├── D00133.002.txt │ ├── D00134.001.txt │ ├── D00135.001.txt │ ├── D00136.001.txt │ ├── D00136.002.txt │ ├── D00137.001.txt │ ├── D00138.001.txt │ ├── D00138.002.txt │ ├── D00139.001.txt │ ├── D00140.001.txt │ ├── D00141.001.txt │ ├── D00142.001.txt │ ├── D00143.001.txt │ ├── D00144.001.txt │ ├── D00145.001.txt │ ├── D00146.001.txt │ ├── D00147.001.txt │ ├── D00148.001.txt │ ├── D00148.002.txt │ ├── D00149.001.txt │ ├── D00149.002.txt │ ├── D00149.003.txt │ ├── D00150.001.txt │ ├── D00151.001.txt │ ├── D00152.001.txt │ ├── D00153.001.txt │ ├── D00154.001.txt │ ├── D00155.001.txt │ ├── D00156.001.txt │ ├── D00157.001.txt │ ├── D00157.002.txt │ ├── D00158.001.txt │ ├── D00159.001.txt │ ├── D00160.001.txt │ ├── D00161.001.txt │ ├── D00162.001.txt │ ├── D00162.002.txt │ ├── D00163.001.txt │ ├── D00163.002.txt │ ├── D00164.001.txt │ ├── D00165.001.txt │ ├── D00166.001.txt │ ├── D00167.001.txt │ ├── D00168.001.txt │ ├── D00168.002.txt │ ├── D00168.003.txt │ ├── D00169.001.txt │ ├── D00169.002.txt │ ├── D00169.003.txt │ ├── D00169.004.txt │ ├── D00169.005.txt │ ├── D00169.006.txt │ ├── D00170.001.txt │ ├── D00171.001.txt │ ├── D00172.001.txt │ ├── D00173.001.txt │ ├── D00174.001.txt │ ├── D00175.001.txt │ ├── D00176.001.txt │ ├── D00177.001.txt │ ├── D00178.001.txt │ ├── D00179.001.txt │ ├── D00180.001.txt │ ├── D00181.001.txt │ ├── D00182.001.txt │ ├── D00183.001.txt │ ├── D00184.001.txt │ ├── D00185.001.txt │ ├── D00186.001.txt │ ├── D00187.001.txt │ ├── D00188.001.txt │ ├── D00189.001.txt │ ├── D00190.001.txt │ ├── D00191.001.txt │ ├── D00192.001.txt │ ├── D00193.001.txt │ ├── D00194.001.txt │ ├── D00195.001.txt │ ├── D00196.001.txt │ ├── D00197.001.txt │ ├── D00198.001.txt │ ├── D00199.001.txt │ ├── D00200.001.txt │ ├── D00201.001.txt │ ├── D00202.001.txt │ ├── D00203.001.txt │ ├── D00204.001.txt │ ├── D00205.001.txt │ ├── D00206.001.txt │ ├── D00207.001.txt │ ├── D00208.001.txt │ ├── D00209.001.txt │ ├── D00210.001.txt │ ├── D00211.001.txt │ ├── D00212.001.txt │ ├── D00213.001.txt │ ├── D00214.001.txt │ ├── D00215.001.txt │ ├── D00216.001.txt │ ├── D00217.001.txt │ ├── D00218.001.txt │ ├── D00219.001.txt │ ├── D00220.001.txt │ ├── D00221.001.txt │ ├── D00222.001.txt │ ├── D00223.001.txt │ ├── D00224.001.txt │ ├── D00225.001.txt │ ├── D00226.001.txt │ ├── D00227.001.txt │ ├── D00228.001.txt │ ├── D00229.001.txt │ ├── D00230.001.txt │ ├── D00231.001.txt │ ├── D00232.001.txt │ ├── D00233.001.txt │ ├── D00234.001.txt │ ├── D00235.001.txt │ ├── D00236.001.txt │ ├── D00237.001.txt │ ├── D00238.001.txt │ ├── D00239.001.txt │ ├── D00240.001.txt │ ├── D00241.001.txt │ ├── D00242.001.txt │ ├── D00243.001.txt │ ├── D00244.001.txt │ ├── D00245.001.txt │ ├── D00246.001.txt │ ├── D00247.001.txt │ ├── D00248.001.txt │ ├── D00249.001.txt │ ├── D00250.001.txt │ ├── D00251.001.txt │ ├── D00252.001.txt │ ├── D00253.001.txt │ ├── D00254.001.txt │ ├── D00255.001.txt │ ├── D00256.001.txt │ ├── D00257.001.txt │ ├── D00258.001.txt │ ├── D00259.001.txt │ ├── D00260.001.txt │ ├── D00261.001.txt │ ├── D00262.001.txt │ ├── D00263.001.txt │ ├── D00264.001.txt │ ├── D00265.001.txt │ ├── D00266.001.txt │ ├── D00267.001.txt │ ├── D00268.001.txt │ ├── D00269.001.txt │ ├── D00270.001.txt │ ├── D00271.001.txt │ ├── D00272.001.txt │ ├── D00273.001.txt │ ├── D00274.001.txt │ ├── D00274.002.txt │ ├── D00275.001.txt │ ├── D00276.001.txt │ ├── D00277.001.txt │ ├── D00278.001.txt │ ├── D00279.001.txt │ ├── D00280.001.txt │ ├── D00281.001.txt │ ├── D00282.001.txt │ ├── D00283.001.txt │ ├── D00284.001.txt │ ├── D00285.001.txt │ ├── D00286.001.txt │ ├── D00287.001.txt │ ├── D00288.001.txt │ ├── D00289.002.txt │ ├── D00290.003.txt │ ├── D00291.002.txt │ ├── D00292.001.txt │ ├── D00293.003.txt │ ├── D00294.001.txt │ ├── D00295.002.txt │ ├── D00296.006.txt │ ├── D00297.002.txt │ ├── D00298.003.txt │ ├── D00299.003.txt │ ├── D00300.003.txt │ ├── D00301.003.txt │ ├── D00302.003.txt │ ├── D00303.002.txt │ ├── D00304.003.txt │ ├── D00305.003.txt │ ├── D00306.003.txt │ ├── D00307.001.txt │ ├── D00308.003.txt │ ├── D00309.002.txt │ ├── D00310.002.txt │ ├── D00311.003.txt │ ├── D00312.002.txt │ ├── D00313.002.txt │ ├── D00314.001.txt │ ├── D00315.003.txt │ ├── D00316.003.txt │ ├── D00317.003.txt │ ├── D00317.009.txt │ ├── D00318.001.txt │ ├── D00318.004.txt │ ├── D00319.003.txt │ ├── D00320.001.txt │ ├── D00321.003.txt │ ├── D00322.002.txt │ ├── D00323.002.txt │ ├── D00324.003.txt │ ├── D00325.003.txt │ ├── D00326.002.txt │ ├── D00327.002.txt │ ├── D00328.003.txt │ ├── D00328.018.txt │ ├── D00329.002.txt │ ├── D00330.002.txt │ ├── D00331.006.txt │ ├── D00332.003.txt │ ├── D00333.004.txt │ ├── D00334.002.txt │ ├── D00335.003.txt │ ├── D00336.001.txt │ ├── D00337.001.txt │ ├── D00338.002.txt │ ├── D00339.002.txt │ ├── D00340.003.txt │ ├── D00341.003.txt │ ├── D00342.003.txt │ ├── D00343.003.txt │ ├── D00344.002.txt │ ├── D00344.005.txt │ ├── D00345.002.txt │ ├── D00346.003.txt │ ├── D00347.003.txt │ ├── D00347.005.txt │ ├── D00348.003.txt │ ├── D00349.002.txt │ ├── D00350.002.txt │ ├── D00350.005.txt │ ├── D00351.001.txt │ ├── D00351.006.txt │ ├── D00351.009.txt │ ├── D00352.002.txt │ ├── D00353.005.txt │ ├── D00354.002.txt │ ├── D00355.002.txt │ ├── D00356.005.txt │ ├── D00356.010.txt │ ├── D00357.002.txt │ ├── D00358.003.txt │ ├── D00359.004.txt │ ├── D00360.004.txt │ ├── D00360.007.txt │ ├── D00361.001.txt │ ├── D00362.002.txt │ ├── D00363.003.txt │ ├── D00363.004.txt │ ├── D00364.002.txt │ ├── D00365.003.txt │ ├── D00366.003.txt │ ├── D00367.003.txt │ ├── D00368.007.txt │ ├── D00369.003.txt │ ├── D00370.003.txt │ ├── D00371.003.txt │ ├── D00372.003.txt │ ├── D00373.003.txt │ ├── D00374.003.txt │ ├── D00375.003.txt │ ├── D00376.003.txt │ ├── D00377.001.txt │ ├── D00378.007.txt │ ├── D00378.009.txt │ ├── D00379.001.txt │ ├── D00380.002.txt │ ├── D00381.003.txt │ ├── D00382.003.txt │ ├── D00383.002.txt │ ├── D00384.002.txt │ ├── D00385.002.txt │ ├── D00386.001.txt │ ├── D00387.001.txt │ ├── D00388.003.txt │ ├── D00389.005.txt │ ├── D00390.002.txt │ ├── D00391.003.txt │ ├── D00392.002.txt │ ├── D00393.003.txt │ ├── D00394.003.txt │ ├── D00395.002.txt │ ├── D00396.003.txt │ ├── D00397.003.txt │ ├── D00398.001.txt │ ├── D00399.002.txt │ ├── D00400.003.txt │ ├── D00401.003.txt │ ├── D00402.001.txt │ ├── D00403.001.txt │ ├── D00404.002.txt │ ├── D00405.003.txt │ ├── D00406.002.txt │ ├── D00407.003.txt │ ├── D00408.003.txt │ ├── D00409.003.txt │ ├── D00409.004.txt │ ├── D00410.003.txt │ ├── D00410.009.txt │ ├── D00411.003.txt │ ├── D00412.002.txt │ ├── D00413.003.txt │ ├── D00414.003.txt │ ├── D00415.003.txt │ ├── D00416.005.txt │ ├── D00417.005.txt │ ├── D00418.003.txt │ ├── D00419.003.txt │ ├── D00420.004.txt │ ├── D00421.003.txt │ ├── D00422.003.txt │ ├── D00423.005.txt │ ├── D00424.002.txt │ ├── D00425.002.txt │ ├── D00426.003.txt │ ├── D00427.003.txt │ ├── D00428.002.txt │ ├── D00429.003.txt │ ├── D00430.003.txt │ ├── D00431.002.txt │ ├── D00432.003.txt │ ├── D00433.003.txt │ ├── D00434.003.txt │ ├── D00435.003.txt │ ├── D00436.002.txt │ ├── D00437.004.txt │ ├── D00438.003.txt │ ├── D00439.003.txt │ ├── D00440.003.txt │ ├── D00441.003.txt │ ├── D00442.003.txt │ ├── D00443.001.txt │ ├── D00444.001.txt │ ├── D00445.003.txt │ ├── D00446.005.txt │ ├── D00446.009.txt │ ├── D00447.002.txt │ ├── D00448.002.txt │ ├── D00449.002.txt │ ├── D00450.003.txt │ ├── D00451.002.txt │ ├── D00452.001.txt │ ├── D00453.002.txt │ ├── D00454.003.txt │ ├── D00455.001.txt │ ├── D00456.001.txt │ ├── D00457.003.txt │ ├── D00458.003.txt │ ├── D00459.003.txt │ ├── D00460.003.txt │ ├── D00461.003.txt │ ├── D00462.002.txt │ ├── D00463.003.txt │ ├── D00464.001.txt │ ├── D00465.003.txt │ ├── D00466.003.txt │ ├── D00467.002.txt │ ├── D00468.003.txt │ ├── D00469.003.txt │ ├── D00470.005.txt │ ├── D00471.002.txt │ ├── D00472.003.txt │ ├── D00473.003.txt │ ├── D00474.003.txt │ ├── D00475.003.txt │ ├── D00475.006.txt │ ├── D00476.002.txt │ ├── D00476.004.txt │ ├── D00477.003.txt │ ├── D00478.003.txt │ ├── D00479.006.txt │ ├── D00480.002.txt │ ├── D00481.003.txt │ ├── D00482.003.txt │ ├── D00483.001.txt │ ├── D00484.003.txt │ ├── D00485.004.txt │ ├── D00486.002.txt │ ├── D00487.003.txt │ ├── D00488.003.txt │ ├── D00489.002.txt │ ├── D00490.003.txt │ ├── D00491.003.txt │ ├── D00492.003.txt │ ├── D00493.003.txt │ ├── D00494.002.txt │ ├── D00495.003.txt │ ├── D00496.002.txt │ ├── D00497.002.txt │ ├── D00498.002.txt │ ├── D00499.001.txt │ ├── D00500.002.txt │ ├── D00501.003.txt │ ├── D00501.004.txt │ ├── D00502.002.txt │ ├── D00503.004.txt │ ├── D00503.014.txt │ ├── D00504.002.txt │ ├── D00504.005.txt │ ├── D00505.003.txt │ ├── D00505.006.txt │ ├── D00506.003.txt │ ├── D00507.002.txt │ ├── D00508.004.txt │ ├── D00509.001.txt │ ├── D00510.003.txt │ ├── D00511.002.txt │ ├── D00512.001.txt │ ├── D00513.002.txt │ ├── D00514.003.txt │ ├── D00515.002.txt │ ├── D00516.002.txt │ ├── D00517.002.txt │ ├── D00518.002.txt │ ├── D00519.002.txt │ ├── D00520.002.txt │ ├── D00521.003.txt │ ├── D00522.002.txt │ ├── D00523.003.txt │ ├── D00524.002.txt │ ├── D00525.002.txt │ ├── D00526.001.txt │ ├── D00527.003.txt │ ├── D00528.001.txt │ ├── D00529.001.txt │ ├── D00529.004.txt │ ├── D00530.003.txt │ ├── D00531.003.txt │ ├── D00532.003.txt │ ├── D00533.003.txt │ ├── D00534.003.txt │ ├── D00534.004.txt │ ├── D00535.003.txt │ ├── D00535.004.txt │ ├── D00536.003.txt │ ├── D00537.001.txt │ ├── D00538.001.txt │ ├── D00539.001.txt │ ├── D00540.002.txt │ ├── D00541.001.txt │ ├── D00542.005.txt │ ├── D00543.005.txt │ ├── D00544.005.txt │ ├── D00545.002.txt │ ├── D00546.003.txt │ ├── D00547.003.txt │ ├── D00548.002.txt │ ├── D00549.002.txt │ ├── D00550.002.txt │ ├── D00551.002.txt │ ├── D00552.002.txt │ ├── D00552.006.txt │ ├── D00553.003.txt │ ├── D00554.003.txt │ ├── D00555.002.txt │ ├── D00556.003.txt │ ├── D00557.002.txt │ ├── D00558.002.txt │ ├── D00559.001.txt │ ├── D00559.006.txt │ ├── D00560.003.txt │ ├── D00561.001.txt │ ├── D00562.006.txt │ ├── D00563.002.txt │ ├── D00564.004.txt │ ├── D00565.002.txt │ ├── D00566.003.txt │ ├── D00567.002.txt │ ├── D00568.001.txt │ ├── D00569.002.txt │ ├── D00570.002.txt │ ├── D00571.002.txt │ ├── D00572.002.txt │ ├── D00573.002.txt │ ├── D00574.002.txt │ ├── D00574.006.txt │ ├── D00575.003.txt │ ├── D00576.005.txt │ ├── D00577.002.txt │ ├── D00578.002.txt │ ├── D00579.002.txt │ ├── D00580.005.txt │ ├── D00581.002.txt │ ├── D00582.001.txt │ ├── D00583.002.txt │ ├── D00584.001.txt │ ├── D00585.003.txt │ ├── D00586.004.txt │ ├── D00587.002.txt │ ├── D00588.002.txt │ ├── D00589.001.txt │ ├── D00589.005.txt │ ├── D00590.001.txt │ ├── D00591.002.txt │ ├── D00592.003.txt │ ├── D00593.003.txt │ ├── D00594.002.txt │ ├── D00595.001.txt │ ├── D00596.005.txt │ ├── D00597.001.txt │ ├── D00598.001.txt │ ├── D00599.006.txt │ ├── D00600.001.txt │ ├── D00600.004.txt │ ├── D00601.003.txt │ ├── D00602.008.txt │ ├── D00603.003.txt │ ├── D00604.004.txt │ ├── D00605.003.txt │ ├── D00606.002.txt │ ├── D00607.006.txt │ ├── D00608.002.txt │ ├── D00609.002.txt │ ├── D00610.003.txt │ ├── D00611.001.txt │ ├── D00612.001.txt │ ├── D00613.002.txt │ ├── D00614.001.txt │ ├── D00615.001.txt │ ├── D00616.002.txt │ ├── D00617.002.txt │ ├── D00618.003.txt │ ├── D00619.003.txt │ ├── D00619.007.txt │ ├── D00620.003.txt │ ├── D00621.003.txt │ ├── D00622.003.txt │ ├── D00623.003.txt │ ├── D00624.007.txt │ ├── D00624.009.txt │ ├── D00625.001.txt │ ├── D00626.005.txt │ ├── D00626.009.txt │ ├── D00627.002.txt │ ├── D00628.002.txt │ ├── D00629.006.txt │ ├── D00630.003.txt │ ├── D00631.002.txt │ ├── D00632.001.txt │ ├── D00633.001.txt │ ├── D00634.001.txt │ ├── D00635.001.txt │ ├── D00636.003.txt │ ├── D00637.003.txt │ ├── D00638.003.txt │ ├── D00639.003.txt │ ├── D00640.003.txt │ ├── D00641.002.txt │ ├── D00642.003.txt │ ├── D00643.002.txt │ ├── D00644.003.txt │ ├── D00645.006.txt │ ├── D00646.002.txt │ ├── D00647.002.txt │ ├── D00648.004.txt │ ├── D00649.002.txt │ ├── D00650.005.txt │ ├── D00650.007.txt │ ├── D00651.003.txt │ ├── D00652.003.txt │ ├── D00652.004.txt │ ├── D00653.003.txt │ ├── D00654.003.txt │ ├── D00655.002.txt │ ├── D00655.006.txt │ ├── D00656.001.txt │ ├── D00657.003.txt │ ├── D00658.003.txt │ ├── D00659.002.txt │ ├── D00660.005.txt │ ├── D00660.007.txt │ ├── D00661.003.txt │ ├── D00662.003.txt │ ├── D00663.002.txt │ ├── D00664.002.txt │ ├── D00665.002.txt │ ├── D00666.002.txt │ ├── D00667.001.txt │ ├── D00668.003.txt │ ├── D00669.002.txt │ ├── D00670.002.txt │ ├── D00671.003.txt │ ├── D00672.001.txt │ ├── D00673.001.txt │ ├── D00674.003.txt │ ├── D00675.001.txt │ ├── D00676.002.txt │ ├── D00677.003.txt │ ├── D00678.001.txt │ ├── D00679.004.txt │ ├── D00680.001.txt │ ├── D00681.002.txt │ ├── D00681.004.txt │ ├── D00682.002.txt │ ├── D00683.002.txt │ ├── D00683.007.txt │ ├── D00684.005.txt │ ├── D00685.003.txt │ ├── D00686.002.txt │ ├── D00687.001.txt │ ├── D00688.002.txt │ ├── D00689.003.txt │ ├── D00690.003.txt │ ├── D00691.001.txt │ ├── D00692.002.txt │ ├── D00693.002.txt │ ├── D00694.003.txt │ ├── D00695.002.txt │ ├── D00696.003.txt │ ├── D00697.002.txt │ ├── D00698.001.txt │ ├── D00699.001.txt │ ├── D00700.001.txt │ ├── D00700.006.txt │ ├── D00701.001.txt │ ├── D00702.001.txt │ ├── D00703.002.txt │ ├── D00704.001.txt │ ├── D00705.003.txt │ ├── D00706.001.txt │ ├── D00707.004.txt │ ├── D00708.001.txt │ ├── D00709.002.txt │ ├── D00710.002.txt │ ├── D00710.007.txt │ ├── D00711.003.txt │ ├── D00712.002.txt │ ├── D00713.003.txt │ ├── D00714.003.txt │ ├── D00714.004.txt │ ├── D00715.002.txt │ ├── D00716.004.txt │ ├── D00717.003.txt │ ├── D00718.002.txt │ ├── D00719.002.txt │ ├── D00720.002.txt │ ├── D00721.002.txt │ ├── D00722.002.txt │ ├── D00723.003.txt │ ├── D00723.006.txt │ ├── D00724.003.txt │ ├── D00725.004.txt │ ├── D00726.003.txt │ ├── D00727.003.txt │ ├── D00728.002.txt │ ├── D00729.003.txt │ ├── D00730.002.txt │ ├── D00731.003.txt │ ├── D00732.005.txt │ ├── D00733.003.txt │ ├── D00734.003.txt │ ├── D00735.002.txt │ ├── D00736.002.txt │ ├── D00737.001.txt │ ├── D00738.002.txt │ ├── D00739.001.txt │ ├── D00740.002.txt │ ├── D00741.001.txt │ ├── D00742.002.txt │ ├── D00743.001.txt │ ├── D00744.001.txt │ ├── D00745.001.txt │ ├── D00746.004.txt │ ├── D00747.001.txt │ ├── D00748.001.txt │ ├── D00749.001.txt │ ├── D00750.001.txt │ ├── D00751.005.txt │ ├── D00752.001.txt │ ├── D00753.001.txt │ ├── D00754.003.txt │ ├── D00755.003.txt │ ├── D00755.005.txt │ ├── D00756.007.txt │ ├── D00757.001.txt │ ├── D00758.001.txt │ ├── D00759.001.txt │ ├── D00760.003.txt │ ├── D00761.001.txt │ ├── D00762.001.txt │ ├── D00763.001.txt │ ├── D00764.001.txt │ ├── D00765.001.txt │ ├── D00766.002.txt │ ├── D00767.001.txt │ ├── D00768.001.txt │ ├── D00769.001.txt │ ├── D00770.002.txt │ ├── D00771.001.txt │ ├── D00772.001.txt │ ├── D00773.001.txt │ ├── D00774.001.txt │ ├── D00775.001.txt │ ├── D00776.005.txt │ ├── D00777.002.txt │ ├── D00778.002.txt │ ├── D00779.001.txt │ ├── D00780.001.txt │ ├── D00781.003.txt │ ├── D00782.001.txt │ ├── D00783.001.txt │ ├── D00784.004.txt │ ├── D00785.001.txt │ ├── D00786.001.txt │ ├── D00787.002.txt │ ├── D00788.001.txt │ ├── D00789.003.txt │ ├── D00790.001.txt │ ├── D00791.001.txt │ ├── D00792.001.txt │ ├── D00793.002.txt │ ├── D00794.047.txt │ ├── D00795.001.txt │ ├── D00796.001.txt │ ├── D00797.001.txt │ ├── D00798.001.txt │ ├── D00799.001.txt │ ├── D00800.001.txt │ ├── D00801.001.txt │ ├── D00802.001.txt │ ├── D00803.002.txt │ ├── D00804.002.txt │ ├── D00805.001.txt │ ├── D00806.003.txt │ ├── D00807.001.txt │ ├── D00808.004.txt │ ├── D00809.002.txt │ ├── D00810.001.txt │ ├── D00811.001.txt │ ├── D00812.001.txt │ ├── D00813.009.txt │ ├── D00814.001.txt │ ├── D00815.001.txt │ ├── D00816.001.txt │ ├── D00817.001.txt │ ├── D00818.003.txt │ ├── D00819.002.txt │ ├── D00820.001.txt │ ├── D00821.001.txt │ ├── D00822.001.txt │ ├── D00823.002.txt │ ├── D00824.001.txt │ ├── D00825.001.txt │ ├── D00826.001.txt │ ├── D00827.001.txt │ ├── D00828.002.txt │ └── D00829.002.txt ├── deepbind ├── example.fa ├── example.ids ├── example.seq └── src ├── a.out ├── deepbind.c ├── deepbind.c~ ├── makefile └── makefile~ /LICENSE.TXT: -------------------------------------------------------------------------------- 1 | BSD 3-clause license: 2 | 3 | Copyright (c) 2014, Andrew Delong. 4 | All rights reserved. 5 | 6 | Redistribution and use in source and binary forms, 7 | with or without modification, are permitted provided 8 | that the following conditions are met: 9 | 10 | 1. Redistributions of source code must retain the 11 | above copyright notice, this list of conditions 12 | and the following disclaimer. 13 | 14 | 2. Redistributions in binary form must reproduce 15 | the above copyright notice, this list of conditions 16 | and the following disclaimer in the documentation 17 | and/or other materials provided with the distribution. 18 | 19 | 3. Neither the name of the copyright holder nor the 20 | names of its contributors may be used to endorse or 21 | promote products derived from this software without 22 | specific prior written permission. 23 | 24 | THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS 25 | "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT 26 | LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR 27 | A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT 28 | HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, 29 | SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT 30 | LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, 31 | DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY 32 | THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 33 | (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE 34 | OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 35 | -------------------------------------------------------------------------------- /README.TXT: -------------------------------------------------------------------------------- 1 | DEEPBIND v0.1 2 | ------------- 3 | 4 | The deepbind command-line executable can be used to score DNA/RNA sequences 5 | according to any RBP/TF model listed in the DeepBind web repository: 6 | 7 | http://tools.genes.toronto.edu/deepbind 8 | 9 | For each input sequence, the deepbind executable scores each subsequence 10 | of a pre-determined length (e.g. 20) and returns only the maximum score over 11 | all positions. 12 | 13 | 14 | EXAMPLE 15 | ------- 16 | 17 | To generate predictions with DeepBind, you need two things: 18 | 19 | 1) a list of model IDs, and 20 | 2) a list of DNA/RNA sequences. 21 | 22 | The file example.ids contains 4 example model IDs, one 23 | on each line, reproduced here: 24 | 25 | D00210.001 # RBFOX1 (RNAcompete) 26 | D00120.001 # MBNL1 (RNAcompete) 27 | D00410.003 # GATA3 (SELEX) 28 | D00328.003 # CTCF (SELEX) 29 | 30 | The file example.seq contains 4 example sequences, which 31 | were chosen such that the nth sequence scores highly for 32 | the nth model. The file example.seq is reproduced here: 33 | 34 | AGGUAAUAAUUUGCAUGAAAUAACUUGGAGAGGAUAGC 35 | AGACAGAGCUUCCAUCAGCGCUAGCAGCAGAGACCAUU 36 | GAGGTTACGCGGCAAGATAA 37 | TACCACTAGGGGGCGCCACC 38 | 39 | To generate 16 predictions (4 models, 4 sequences), run 40 | the deepbind executable as follows: 41 | 42 | % deepbind example.ids < example.seq 43 | D00210.001 D00120.001 D00410.003 D00328.003 44 | 7.345649 -0.152710 -0.763340 -0.026180 45 | -0.159393 3.663924 -0.196943 -0.026180 46 | -0.143584 0.357632 5.885349 -0.026180 47 | -0.161033 -0.081444 -0.379695 17.682623 48 | 49 | To see details of each ID, use the --dump-info flag: 50 | 51 | % deepbind --dump-info example.ids 52 | ID Protein Type Species Family Class Experiment ... 53 | D00210.001 RBFOX1 RBP Homo sapiens RRM RNAcompete ... 54 | D00120.001 MBNL1 RBP Homo sapiens Znf RNAcompete ... 55 | D00410.003 GATA3 TF Homo sapiens GATA SELEX ... 56 | D00328.003 CTCF TF Homo sapiens znfC2H2 SELEX ... 57 | -------------------------------------------------------------------------------- /README_IMK.md: -------------------------------------------------------------------------------- 1 | # deepbind 2 | I have put my modified version of the deepbind code here. 3 | 4 | Here are the changes that I have made from the original deepbind code: 5 | * The original code did not score the last position in the sequence. I have fixed this bug. 6 | * The original code checks every model to see if the reverse complement should be scored. If it should, it gets the reverse complement of the sequence and scores it. As a result, it gets the reverse complement of the sequence separately for every model. I have changed it to assume that the reverse complement should be scored and get the reverse complement of the sequence before iterating through the models. 7 | * I have added an --all-scores option that prints the score at every position instead of the maximum score across the sequence. At each position, it prints the maximum of the score for the sequence and its reverse complement. 8 | * I have added a --class-prob option that gets the probability of each sequence being a TF-binding site for each model instead of printing the output of the fully-connected layer for each model. It does this by running the output of the fully-connected layer through a sigmoid. 9 | -------------------------------------------------------------------------------- /db/params/D00169.006.txt: -------------------------------------------------------------------------------- 1 | # deepbind 0.1 2 | reverse_complement = 0 3 | num_detectors = 16 4 | detector_len = 16 5 | has_avg_pooling = 1 6 | num_hidden = 0 7 | detectors = 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8 | thresholds = -7.740070578e-05,-1.363906078e-03,-8.337937761e-04,-8.553519845e-01,-2.815182321e-03,-6.884394679e-04,-1.344614546e-03,-9.333087946e-04,-8.952239878e-04,-2.332164440e-03,-6.657544291e-04,4.643051216e-05,-3.338347655e-03,-1.801207196e-03,-3.287974396e-04,-9.091809625e-04 9 | weights1 = 1.268278575e-03,-8.871795144e-04,2.413386013e-03,5.685576238e-03,-3.126255935e-03,-6.277916022e-03,8.084012270e-01,8.069903851e-01,6.595858373e-03,9.800996631e-03,-6.842081901e-03,-9.532303666e-04,4.627500195e-03,-6.161275320e-03,-3.183040069e-03,-1.077244640e-03,-3.069838276e-03,1.013112161e-02,-2.657847945e-03,-1.026436407e-02,-3.858245909e-03,-5.716102896e-04,1.851162873e-03,-1.856621122e-03,6.123703439e-03,5.796939600e-03,4.929355346e-03,3.819842823e-03,1.679310342e-03,-6.413903553e-03,-3.284227103e-03,1.087460108e-02 10 | biases1 = -1.792288870e-01 11 | weights2 = 12 | biases2 = 13 | -------------------------------------------------------------------------------- /db/params/D00344.002.txt: -------------------------------------------------------------------------------- 1 | # deepbind 0.1 2 | reverse_complement = 1 3 | num_detectors = 16 4 | detector_len = 14 5 | has_avg_pooling = 0 6 | num_hidden = 0 7 | detectors = 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8 | thresholds = -1.593867391e-01,-2.115275311e-05,-3.110824764e-05,-6.115686893e-01,-7.044484615e-01,-1.070953757e-01,-1.172305201e-04,-3.726508617e-01,-2.454785317e-05,-8.417474031e-01,-1.494781077e-01,-4.917035039e-05,-4.369828403e-01,-1.183156446e-01,-1.042758003e-01,-1.693969220e-01 9 | weights1 = 2.470028996e-01,-4.696590339e-12,-2.724852982e-11,6.271245480e-01,7.022677660e-01,1.885313392e-01,2.186850458e-02,3.866207600e-01,1.839555765e-11,8.152196407e-01,2.289226353e-01,1.632818186e-11,5.218316913e-01,2.025454044e-01,2.493667305e-01,2.232786417e-01 10 | biases1 = -2.261623740e-01 11 | weights2 = 12 | biases2 = 13 | -------------------------------------------------------------------------------- /db/params/D00347.003.txt: -------------------------------------------------------------------------------- 1 | # deepbind 0.1 2 | reverse_complement = 1 3 | num_detectors = 16 4 | detector_len = 14 5 | has_avg_pooling = 0 6 | num_hidden = 0 7 | detectors = 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8 | thresholds = -1.169180125e-01,-6.890302151e-02,-1.287976056e-01,-2.122217268e-01,-7.848846912e-02,-9.972362965e-02,-6.534738839e-02,-1.363951266e-01,-1.947617233e-01,-7.801100612e-02,-1.962131709e-01,-6.869567186e-02,-1.382802576e-01,-1.452737600e-01,-1.644176245e-01,-1.739227921e-01 9 | weights1 = 3.259527683e-01,2.484904528e-01,3.346587718e-01,3.672447801e-01,2.533402741e-01,3.132351637e-01,2.576118112e-01,3.637921214e-01,3.822959065e-01,2.100916356e-01,3.965079784e-01,2.277591377e-01,3.428165019e-01,3.592591286e-01,3.365139961e-01,4.221979082e-01 10 | biases1 = -6.299507022e-01 11 | weights2 = 12 | biases2 = 13 | -------------------------------------------------------------------------------- /db/params/D00349.002.txt: -------------------------------------------------------------------------------- 1 | # deepbind 0.1 2 | reverse_complement = 1 3 | num_detectors = 16 4 | detector_len = 14 5 | has_avg_pooling = 0 6 | num_hidden = 0 7 | detectors = 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8 | thresholds = -2.204852935e-04,-1.005139668e-02,-1.786297411e-01,-9.906133637e-04,-1.234624506e-04,-9.618879994e-04,-4.138207587e-04,-2.091227943e-04,-9.596828371e-02,-6.532078260e-04,-1.299327761e-01,-6.996259838e-02,-9.135653824e-02,-1.224183887e-01,-8.930017054e-02,-8.930962533e-02 9 | weights1 = -4.443224752e-04,4.073753208e-02,4.195421040e-01,-4.698038567e-03,-1.962581209e-09,-4.539514426e-03,-1.511384966e-03,-3.815633245e-04,2.909731567e-01,-2.832491416e-03,3.764095604e-01,2.930033505e-01,2.758277655e-01,2.916553319e-01,2.926050425e-01,3.686386049e-01 10 | biases1 = -6.352893114e-01 11 | weights2 = 12 | biases2 = 13 | -------------------------------------------------------------------------------- /db/params/D00375.003.txt: -------------------------------------------------------------------------------- 1 | # deepbind 0.1 2 | reverse_complement = 1 3 | num_detectors = 16 4 | detector_len = 14 5 | has_avg_pooling = 0 6 | num_hidden = 0 7 | detectors = 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8 | thresholds = -2.385102063e-01,-1.459904597e-04,-1.740967780e-01,-6.315899373e-05,-1.995483041e+00,-1.534031034e-01,-1.315819682e-04,-2.906159870e-02,-8.121960127e-05,-6.606190436e-05,-7.048600673e-05,-3.245073458e-05,-8.289994003e-05,-2.203450799e-01,-1.781516522e-01,-2.500878572e-01 9 | weights1 = 5.106108189e-01,-1.133893384e-03,4.841926992e-01,-1.010602573e-04,2.556527853e+00,5.635091066e-01,-8.670127718e-04,1.089613959e-01,-2.731842978e-04,-5.114485393e-04,-7.523349632e-05,-2.202105134e-05,-3.114181454e-04,5.892440677e-01,4.545238614e-01,5.732334256e-01 10 | biases1 = -9.509696364e-01 11 | weights2 = 12 | biases2 = 13 | -------------------------------------------------------------------------------- /db/params/D00388.003.txt: -------------------------------------------------------------------------------- 1 | # deepbind 0.1 2 | reverse_complement = 1 3 | num_detectors = 16 4 | detector_len = 14 5 | has_avg_pooling = 0 6 | num_hidden = 0 7 | detectors = 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8 | thresholds = -1.745558227e-03,-2.687315689e-03,-9.125950933e-01,-4.796218709e-04,-6.041628122e-01,-2.181373537e-01,-1.314080805e-01,-1.106309667e-01,-3.185040653e-01,-9.405916929e-02,-1.575015306e+00,-1.142346533e-03,-4.407204688e-01,-1.629829556e-01,-7.749081254e-01,-1.279365718e-01 9 | weights1 = -1.435747487e-03,-8.323441260e-03,1.073392510e+00,4.934345293e-11,4.955705106e-01,2.934905589e-01,3.327961862e-01,2.615822554e-01,2.935729623e-01,2.665137947e-01,1.873576403e+00,-2.338048536e-03,3.604052365e-01,3.327392042e-01,8.252000809e-01,1.894453466e-01 10 | biases1 = -9.451868534e-01 11 | weights2 = 12 | biases2 = 13 | -------------------------------------------------------------------------------- /db/params/D00391.003.txt: -------------------------------------------------------------------------------- 1 | # deepbind 0.1 2 | reverse_complement = 1 3 | num_detectors = 16 4 | detector_len = 14 5 | has_avg_pooling = 0 6 | num_hidden = 0 7 | detectors = 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8 | thresholds = -1.923314780e-01,-1.035408396e-02,-1.441906095e-01,-5.149762705e-02,-8.292201757e-01,-1.638081670e-01,-7.239553612e-03,-1.404068917e-01,-3.706829855e-03,-4.778236151e-03,-1.487500370e-01,-8.855594695e-02,-4.776101094e-03,-2.474136651e-01,-1.269477367e+00,-1.532472521e-01 9 | weights1 = 5.015606880e-01,-5.559742111e-10,4.871268570e-01,2.239219993e-01,1.101552248e+00,4.741094708e-01,-3.142810456e-08,4.553366005e-01,4.771241624e-09,4.044494073e-09,4.394831061e-01,3.158975542e-01,1.687857676e-08,4.978674352e-01,1.597987533e+00,4.579417706e-01 10 | biases1 = -1.406138062e+00 11 | weights2 = 12 | biases2 = 13 | -------------------------------------------------------------------------------- /db/params/D00401.003.txt: -------------------------------------------------------------------------------- 1 | # deepbind 0.1 2 | reverse_complement = 1 3 | num_detectors = 16 4 | detector_len = 14 5 | has_avg_pooling = 0 6 | num_hidden = 0 7 | detectors = 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8 | thresholds = -2.518647909e-01,-5.052193999e-01,-9.117917418e-01,-2.061832696e-01,-2.957572341e-01,-2.162387818e-01,-2.584410310e-01,-2.272405922e-01,-1.741409600e-01,-2.899242342e-01,-2.924654782e-01,-3.535045981e-01,-4.433504939e-01,-7.047889829e-01,-1.730797589e-01,-2.449957579e-01 9 | weights1 = 4.136205912e-01,5.986630917e-01,8.479424715e-01,3.228823543e-01,4.749851227e-01,3.805718422e-01,3.812900782e-01,3.569383323e-01,2.821452022e-01,4.226166010e-01,4.272530675e-01,3.814584613e-01,5.268749595e-01,6.616456509e-01,3.370678723e-01,3.942047358e-01 10 | biases1 = -4.760270417e-01 11 | weights2 = 12 | biases2 = 13 | -------------------------------------------------------------------------------- /db/params/D00430.003.txt: -------------------------------------------------------------------------------- 1 | # deepbind 0.1 2 | reverse_complement = 1 3 | num_detectors = 16 4 | detector_len = 14 5 | has_avg_pooling = 0 6 | num_hidden = 0 7 | detectors = 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8 | thresholds = -5.166728422e-02,-1.687116772e-01,-1.318614464e-03,-1.866942330e-04,-1.694253385e-01,-2.863793373e-01,-1.057945132e+00,-4.914729595e-01,-2.851484460e-04,-1.462082863e-01,-7.307378203e-02,-1.663609780e-02,-5.636160821e-02,-3.048531711e-02,-1.050340831e-01,-2.420930832e-04 9 | weights1 = 2.147508562e-01,4.482515454e-01,-4.126625299e-06,-1.353530710e-08,5.330086350e-01,4.481487870e-01,1.491318107e+00,6.962330937e-01,1.214641898e-08,4.974419177e-01,3.193719983e-01,9.303796291e-02,2.439639270e-01,1.022402123e-01,5.052763224e-01,1.115151083e-08 10 | biases1 = -6.438412070e-01 11 | weights2 = 12 | biases2 = 13 | -------------------------------------------------------------------------------- /db/params/D00465.003.txt: -------------------------------------------------------------------------------- 1 | # deepbind 0.1 2 | reverse_complement = 1 3 | num_detectors = 16 4 | detector_len = 14 5 | has_avg_pooling = 0 6 | num_hidden = 0 7 | detectors = 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8 | thresholds = -1.915975958e-01,-1.346052766e+00,-3.484776826e-04,-1.618721290e-04,-1.425327063e-01,-1.931434721e-01,-3.120129404e-04,-3.051840514e-02,-1.350503713e-01,-1.866753399e-01,-2.009304762e-01,-1.190497950e-01,-2.076207456e-04,-5.966823101e-01,-1.553748443e-04,-7.611344755e-02 9 | weights1 = 5.280911326e-01,1.769386649e+00,-2.259716392e-03,-1.023792196e-03,4.502459168e-01,4.460856915e-01,-2.018520609e-03,4.757300019e-02,4.397833645e-01,5.649842024e-01,5.560617447e-01,4.009132087e-01,-1.326289843e-03,7.395696640e-01,-9.808099130e-04,1.664073765e-01 10 | biases1 = -1.118196130e+00 11 | weights2 = 12 | biases2 = 13 | -------------------------------------------------------------------------------- /db/params/D00474.003.txt: -------------------------------------------------------------------------------- 1 | # deepbind 0.1 2 | reverse_complement = 1 3 | num_detectors = 16 4 | detector_len = 14 5 | has_avg_pooling = 0 6 | num_hidden = 0 7 | detectors = 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8 | thresholds = -2.854669988e-01,-7.604256272e-01,-3.830105125e-04,-2.202065371e-04,-2.230232358e-01,-1.992007494e-01,-4.119244986e-04,9.061073069e-04,-2.903352380e-01,-6.991330385e-01,-2.232748866e-01,-6.783707440e-02,-3.431436198e-04,-5.534311533e-01,-2.491828054e-04,-6.641703844e-02 9 | weights1 = 3.493353724e-01,7.193689346e-01,-1.541781369e-09,-9.849931537e-09,2.766829729e-01,2.995496392e-01,-1.380216719e-09,2.086412223e-06,3.008236289e-01,6.974396706e-01,2.616800368e-01,1.617933512e-01,-4.642580986e-09,5.208393931e-01,-3.833028561e-09,1.019072682e-01 10 | biases1 = -1.845777929e-01 11 | weights2 = 12 | biases2 = 13 | -------------------------------------------------------------------------------- /db/params/D00625.001.txt: -------------------------------------------------------------------------------- 1 | # deepbind 0.1 2 | reverse_complement = 1 3 | num_detectors = 16 4 | detector_len = 14 5 | has_avg_pooling = 0 6 | num_hidden = 0 7 | detectors = 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8 | thresholds = -3.959438205e-01,-1.963134259e-01,-4.591539204e-01,-1.326671839e-01,-2.337019891e-01,-4.883357286e-01,-4.423505366e-01,-2.246781439e-01,-5.290621519e-01,-5.098919868e-01,-1.770794690e-01,-5.820523500e-01,-2.639067173e-01,-1.686067134e-01,-5.058010817e-01,-2.144881934e-01 9 | weights1 = 3.572474122e-01,2.326380908e-01,4.107384682e-01,1.800637841e-01,2.718980610e-01,4.677122533e-01,4.004212618e-01,2.921558022e-01,4.699799418e-01,4.656915069e-01,2.520981729e-01,5.704457760e-01,2.552700341e-01,2.252780795e-01,4.995009303e-01,2.664267421e-01 10 | biases1 = -2.130385637e-01 11 | weights2 = 12 | biases2 = 13 | -------------------------------------------------------------------------------- /db/params/D00627.002.txt: -------------------------------------------------------------------------------- 1 | # deepbind 0.1 2 | reverse_complement = 1 3 | num_detectors = 16 4 | detector_len = 14 5 | has_avg_pooling = 0 6 | num_hidden = 0 7 | detectors = 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8 | thresholds = -2.204703924e-04,-6.603222340e-02,-4.801202158e-04,-2.280141925e-04,-7.610117644e-02,-1.026030034e-01,-1.888449333e-04,-4.516929761e-02,-6.580523401e-02,-9.815924615e-02,-3.832956718e-04,-1.085434109e-01,-1.026485115e-01,-1.780541241e-01,-9.536921978e-02,-2.890017058e-04 9 | weights1 = -9.989339014e-05,1.411163062e-01,-3.047926293e-04,-4.264403469e-05,2.086550891e-01,2.448930144e-01,-4.612540215e-05,1.330721378e-01,2.054671645e-01,2.847175300e-01,-2.564444731e-04,2.867338657e-01,2.902227044e-01,3.734522462e-01,2.893094122e-01,-1.851468987e-04 10 | biases1 = -3.151378930e-01 11 | weights2 = 12 | biases2 = 13 | -------------------------------------------------------------------------------- /db/params/D00733.003.txt: -------------------------------------------------------------------------------- 1 | # deepbind 0.1 2 | reverse_complement = 1 3 | num_detectors = 16 4 | detector_len = 14 5 | has_avg_pooling = 0 6 | num_hidden = 0 7 | detectors = 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8 | thresholds = -1.407970637e-01,-1.219574884e-01,-1.572785825e-01,-2.174761742e-01,-2.877556346e-02,5.931591988e-02,-1.827630401e-01,-1.107627228e-01,-1.579701453e-01,-1.389807314e-01,-1.861400157e-01,-8.446947485e-02,-1.614675820e-01,-2.540771365e-01,-2.668730542e-02,-1.851645112e-01 9 | weights1 = 1.435265094e-01,1.563807726e-01,1.947690099e-01,2.394637167e-01,1.257654428e-01,4.864710569e-02,2.184723169e-01,1.589321792e-01,1.722043157e-01,2.131680250e-01,2.498226911e-01,1.512127966e-01,1.688736230e-01,2.667284906e-01,1.065528393e-01,2.489357591e-01 10 | biases1 = -1.776121706e-01 11 | weights2 = 12 | biases2 = 13 | -------------------------------------------------------------------------------- /deepbind: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kundajelab/deepbind/714d552fd9808a37a4445049ab4bbb235995f0bd/deepbind -------------------------------------------------------------------------------- /example.fa: -------------------------------------------------------------------------------- 1 | >RBFOX1 test sequence 2 | AGGUAAUAAUUUGCAUGAAAUAACUUGGAGA 3 | GGAUAGC 4 | >MBNL1 test sequence 5 | AGACAGAGCUUCCAUCAGCGCUAGCAGCAGA 6 | GACCAUU 7 | >GATA3 test sequence 8 | GAGGTTACGCGGCAAGATAA 9 | >CTCF test sequence 10 | TACCACTAGGGGGCGCCACC 11 | -------------------------------------------------------------------------------- /example.ids: -------------------------------------------------------------------------------- 1 | D00210.001 # RBFOX1 (RNAcompete) 2 | D00120.001 # MBNL1 (RNAcompete) 3 | D00410.003 # GATA3 (SELEX) 4 | D00328.003 # CTCF (SELEX) -------------------------------------------------------------------------------- /example.seq: -------------------------------------------------------------------------------- 1 | AGGUAAUAAUUUGCAUGAAAUAACUUGGAGAGGAUAGC 2 | AGACAGAGCUUCCAUCAGCGCUAGCAGCAGAGACCAUU 3 | GAGGTTACGCGGCAAGATAA 4 | TACCACTAGGGGGCGCCACC 5 | -------------------------------------------------------------------------------- /src/a.out: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kundajelab/deepbind/714d552fd9808a37a4445049ab4bbb235995f0bd/src/a.out -------------------------------------------------------------------------------- /src/makefile: -------------------------------------------------------------------------------- 1 | SHELL := /bin/bash 2 | 3 | all: ../deepbind 4 | 5 | ../deepbind: deepbind.c 6 | @gcc -o ../deepbind -O3 -DNDEBUG -Wno-unused-result -Wno-format-security deepbind.c -lm 7 | 8 | clean: 9 | @rm ../deepbind 10 | -------------------------------------------------------------------------------- /src/makefile~: -------------------------------------------------------------------------------- 1 | SHELL := /bin/bash 2 | 3 | all: ../deepbind 4 | 5 | ../deepbind: deepbind.c 6 | @gcc -o ../deepbind -lm -O3 -DNDEBUG -Wno-unused-result -Wno-format-security deepbind.c 7 | 8 | clean: 9 | @rm ../deepbind 10 | --------------------------------------------------------------------------------