Use the program:

global$-$align.sh

to globally align THISLINE and ISALIGNED with the BLOSUM$30$ substitution matrix. To do this, you will need to specify the BLOSUM$30$ matrix as an argument after the $-$data flag in the command. For example, you will need to add:

$-$data $/$data$/$compres$/$aligners$/$BLOSUM$30$

The output should look like:

a $1$ THIS$--$LINE$-8$

$||$ :$.||$

b $1--$ISALIGNED $9$

Now, confirm by hand using the BLOSUM$30$ matrix the math that results in the same score as the global alignment script.

Please input the BLOSUM$30$ alignment score values below for each of the aligned columns from the alignment above $($and think about how the BLOSUM$30$ matrix treats end gaps$).$

T to Gap is

H to Gap is

I to I is

S to S is

Gap and A is

Gap to L is

L to I is

I to G is

N to N is

E to E is

Gap to D is

The total alignment score is:

Note: To run global$-$align.sh you may need to make sure the emboss package is also installed $($it is a dependency$).$ To do this, check for the available versions, then load the most recent.

module avail emboss