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-- %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.

for example:

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

I	Attachment	Action	Size	Date	Who	Comment
txt	blosum62.txt	manage	1.5 K	2011-11-12 - 18:10	TaiNg	blosum62 matrix
EXT	blosum_screwup1	manage	1.5 K	2011-11-12 - 18:13	TaiNg
EXT	blosum_screwup2	manage	1.5 K	2011-11-12 - 18:13	TaiNg
EXT	blosum_screwup3	manage	1.5 K	2011-11-12 - 18:13	TaiNg
txt	dna.txt	manage	0.9 K	2011-11-12 - 18:12	TaiNg	dna test file
txt	dnaMatrix.txt	manage	0.1 K	2011-11-12 - 18:12	TaiNg	dna matrix
txt	hw4.pl.txt	manage	8.2 K	2011-11-12 - 23:20	TaiNg
txt	protein.txt	manage	0.1 K	2011-11-12 - 18:12	TaiNg	protein test