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Find an ungapped pattern window from a set of protein sequences

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Find an ungapped pattern window from a set of protein sequences

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05 Dec 2011 (Updated )

This program is to find an ungapped pattern window of certain width from a set of protein sequences

load_DM_1.m
'recode4_20comp',
% Mixed Dirichlet prior for Protein --- Stephen 1
 a = [3.83048e-01,1.74635e-01,8.52555e-02,5.94628e-02,4.06419e-02,3.98597e-02,2.97682e-02,2.80806e-02,2.42095e-02,1.92440e-02,...
      1.78775e-02,1.74343e-02,1.68758e-02,1.39663e-02,1.23711e-02,1.23012e-02,1.11316e-02,6.98083e-03,3.65577e-03,3.20122e-03];
 %    A               R            N           D            C             Q          E            G            H            I             L           K            M            F           P             S            T            W             Y           V          
 al_pha = ...
  [3.35796e-01, 3.07135e-01, 2.29520e-01, 2.70793e-01, 2.76254e-02, 2.54750e-01,3.48046e-01, 2.25768e-01, 1.15656e-01, 1.20617e-01, 2.17130e-01, 3.95388e-01, 6.92591e-02, 8.63198e-02, 1.59096e-01, 2.75135e-01, 2.65742e-01, 4.38520e-02, 1.17411e-01, 1.82309e-01,
   2.73194e-01, 5.45329e-02, 4.45531e-02, 3.65618e-02, 6.47217e-02, 5.01930e-02,4.48084e-02, 7.96421e-02, 3.93740e-02, 5.22913e-01, 8.64337e-01, 4.61325e-02, 1.83843e-01, 2.66448e-01, 6.09869e-02, 7.36139e-02, 1.36326e-01, 5.70540e-02, 1.32732e-01, 5.33931e-01,
   5.91100e-02, 2.60000e-02, 4.30017e-02, 7.85758e-02, 1.27852e-02, 1.27304e-02,3.63021e-02, 1.60842e-01, 2.81857e-02, 1.30422e-02, 2.67507e-02, 2.03385e-02, 3.97971e-03, 2.89509e-02, 6.89402e-02, 6.05953e-02, 4.23799e-02, 1.25806e-02, 3.41105e-02, 3.40264e-02,
   2.29698e+00, 1.35953e-01, 1.46610e-01, 1.55901e-01, 2.65451e-01, 1.27139e-01, 1.71394e-01, 8.69853e-01, 1.02854e-01, 5.14941e-01, 7.59599e-01, 6.95931e-02, 2.34631e-01, 3.86700e-01, 1.77732e-01, 7.49770e-01, 4.57832e-01, 9.86083e-02, 3.12162e-01, 1.05026e+00,
   3.26115e+00, 1.66020e+00, 3.68427e+00, 3.18917e+00, 7.45759e-01, 1.47000e+00, 2.67227e+00, 4.55029e+00, 3.01435e+00, 2.39119e+00, 4.38827e+00, 7.06970e-01, 1.29158e+00, 4.15961e+00, 1.80724e+00, 3.67109e+00, 2.30334e+00, 2.05938e+00, 3.83840e+00, 2.75308e+00,
   1.21186e+01, 1.07077e+01, 2.19455e+00, 3.87403e+00, 4.72681e-01, 4.18394e+00, 6.50480e+00, 2.97363e+00, 1.67069e+00, 8.55045e+00, 1.36136e+01, 9.64583e+00, 3.75321e+00, 3.46117e+00, 1.68259e+00, 2.96826e+00, 3.09571e+00, 1.72721e+00, 4.32637e+00, 8.18250e+00,
   1.02085e+01, 1.49944e+00, 2.36645e+00, 2.52751e+00, 1.74070e+00, 2.74109e+00, 1.66695e+00, 2.93189e+00, 2.32366e+00, 7.70740e+00, 1.24467e+01, 1.63543e+00, 3.31910e+00, 4.64628e+00, 9.15427e-01, 2.30864e+00, 3.94574e+00, 8.65209e-01, 3.17628e+00, 7.72884e+00,
   1.69321e+00, 2.85794e-01, 2.00578e-01, 2.42201e-01, 5.61402e-01, 1.66355e-01, 1.63758e-01, 4.26017e-01, 2.17733e-01, 9.19979e+00, 3.00267e+00, 3.65122e-01, 4.70859e-01, 1.32840e+00, 4.54379e-01, 5.66137e-01, 1.17851e+00, 1.82001e-01, 7.24889e-01, 1.28947e+01,
   6.99016e-01, 1.95050e-01, 7.00959e-01, 5.64493e-01, 1.23918e-01, 3.41402e-01, 4.41809e-01, 4.55207e-01, 1.57372e-01, 4.52220e-01, 2.85096e-01, 3.15356e-01, 1.12360e-01, 2.65585e-01, 3.84523e-01, 3.04705e+00, 3.86283e+00, 7.47102e-02, 2.98617e-01, 7.71455e-01,
   2.69506e+00, 5.28848e-01, 1.20003e+00, 9.99399e-01, 9.84665e-02, 4.85106e-01, 7.02161e-01, 1.47923e+01, 2.04418e-01, 3.41519e-01, 6.04879e-01, 8.95261e-01, 2.64405e-01, 1.88280e-01, 5.26937e-01, 1.54988e+00, 7.59294e-01, 1.15940e-01, 3.30426e-01, 2.20308e-01,
   3.07208e+00, 1.07904e+00, 1.17791e+00, 1.59068e+00, 1.79581e-01, 8.31189e-01, 1.18020e+00, 1.82765e+00, 2.99515e-01, 1.57850e+00, 2.48759e+00, 2.07133e+00, 1.88600e-01, 1.04447e+00, 1.38668e+01, 2.36316e+00, 1.88465e+00, 2.74462e-01, 8.30750e-01, 2.35323e+00,
   1.41269e+00, 3.53594e-01, 2.80603e-01, 3.37209e+00, 5.65739e-03, 1.48884e+00, 5.65739e+00, 6.14150e-01, 1.21496e-01, 1.54197e-01, 4.94589e-01, 7.67153e-01, 1.55884e-01, 2.44139e-01, 2.63088e-01, 1.00131e+00, 5.38288e-01, 7.28146e-02, 2.03510e-01, 3.35960e-01,
   3.33374e+00, 2.43658e+00, 2.10234e+00, 1.93175e+00, 1.15604e+00, 1.36967e+00, 1.30643e+00, 2.12633e+01, 2.00541e+00, 9.73505e+00, 5.17488e+00, 1.95251e+00, 3.25167e+00, 4.97546e+00, 3.30810e+00, 2.02859e+00, 5.17926e+00, 1.61701e+00, 4.40200e+00, 7.52289e+00,
   2.53998e+00, 1.59930e+00, 1.10338e+01, 6.22299e+00, 6.41820e-01, 1.38371e+00, 1.78980e+00, 9.70006e+00, 1.57777e+00, 3.58056e-01, 1.25521e+00, 2.07334e+00, 4.10731e-01, 1.14222e+00, 3.16446e+00, 9.83971e+00, 1.71336e+00, 4.28225e-01, 1.14954e+00, 4.18670e-01,
   2.50469e+01, 1.28818e+01, 6.64437e+00, 1.41297e+01, 2.87555e-02, 1.44893e+01, 2.33767e+01, 5.28742e+00, 2.81354e+00, 1.20677e+00, 4.13300e+00, 2.87555e+01, 1.51853e-01, 5.57453e-01, 2.01447e+00, 1.09112e+01, 3.32116e+00, 4.87539e-02, 5.40820e-01, 1.02430e+00,
   1.50426e+00, 6.28562e-01, 5.72791e+00, 1.52516e+01, 1.06938e-01, 7.25283e-01, 2.40265e+00, 1.80122e+00, 5.05069e-01, 6.74739e-01, 7.28632e-01, 1.40725e+00, 2.37147e-01, 3.29304e-01, 7.39360e-01, 2.17878e+00, 1.44031e+00, 1.52516e-02, 2.83625e-01, 8.11792e-01,
   4.85358e-01, 3.67824e-01, 2.23577e-01, 1.32386e-01, 1.20765e-01, 2.47041e-01, 2.23250e-01, 2.90926e-01, 5.36354e-01, 4.48205e-01, 8.17340e-01, 2.40466e-01, 2.16503e-01, 2.74084e+00, 1.41958e-01, 4.70015e-01, 4.41281e-01, 6.35744e-01, 7.73963e+00, 8.03322e-01,
   4.22519e-01, 1.25594e-02, 7.60594e-02, 6.31780e-02, 1.62589e-01, 1.56490e-01, 2.32174e-01, 1.98806e-01, 1.35336e-01, 5.89954e-01, 1.13028e+00, 1.27259e-01, 2.13526e-01, 8.82940e+00, 1.40012e-01, 3.30880e-01, 3.31744e-01, 9.09754e-01, 2.28988e+00, 6.24835e-01,
   3.50372e-01, 3.56382e-01, 9.44224e-02, 7.20512e-02, 1.13692e-01, 9.63917e-02, 2.10516e-01, 2.58305e-01, 1.30860e-01, 4.35950e-01, 1.31274e+00, 1.53330e-01, 3.21490e-01, 1.25290e+00, 9.66389e-02, 2.06486e-01, 1.67836e-01, 1.35500e+01, 1.07893e+00, 5.82403e-01,
   1.61616e-01, 2.81472e-02, 4.40255e-02, 2.81472e-02, 2.81472e+01, 2.81472e-02, 2.81472e-02, 2.81472e-02, 2.81472e-02, 2.20459e-01, 5.27309e-02, 2.81472e-02, 2.81472e-02, 2.67120e-01, 2.81472e-02, 1.52965e-01, 8.86627e-02, 9.47103e-02, 5.63106e-02, 4.56531e-01];

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