In this practical you will have to write a simple Perl script for performing a hydrophobicity analysis of membrane proteins. The program should read the sequence and create overlapping windows (the size can be variable from 5 to 20). For each window along the sequence the mean hydrophobicity will be calculated and its value will be assigned for simplicity to the middle residue (i.e. for a window with length 5 centered around residue i, the window will take values i-2, i-1, i, i+1 and i+2). Thus, the final "average" hydrophobicity assigned to residue i will be: where h(i) is the hydrophobicity of the residue i given by any of the standard scales. The Kyte-Doolitle hydrophobicity scale: %hyd =('A' => 0.100, 'C' => -1.420, 'D' => 0.780, 'E' => 0.830, 'F' => -2.120, 'G' => 0.330, 'H' => -0.500, 'I' => -1.130, 'K' => 1.400, 'L' => -1.180, 'M' => -1.590, 'N' => 0.480, 'P' => 0.730, 'Q' => 0.950, 'R' => 1.910, 'S' => 0.520, 'T' => 0.070, 'V' => -1.270, 'W' => -0.510, 'Y' => -0.210 ); Hints:
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