-- %TEACHINGWEB%.TaiNg - 03 Nov 2011
How to use implement the program.
In command window, type
hw4.pl MATRIXFILE SEQUENCEFILE POSITION1 POSITION2
By default it will read in the first two sequence in the file.
hw4.pl blosum62.txt protein.txt 0 1
you will get the first and second sequence from protein.txt file.
Make sure no extra space between the program, matrix file, sequence file, position1, and position2.
Below are test files.
dna.txt 0 1 contains the test sequence given in assignment
dna.txt 2 3 contains sequences that test it will print out 80 per line
dnaMatrix.txt is the matrix given in assignment
blosum62.txt is the matrix given in assignment
protein.txt 0 1 contains the sequences given in assignment
blosum_screwup1 contains a matrix file with an extra column
blosum_screwup2 contains a matrix file with extra row
blosum_screwup3 contains a matrix file with extra space in score line
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