I. Two-dimensional arrays

A two-dimensional array can be thought of as a table. Here's one:
 

0

1

2

3

4

5

6

7

8

9

10

11

12

13

14

15

16

17

0

A

A

A

G

T

T

G

T

A

G

T

T

T

C

T

G

T

T

1

T

T

T

T

T

A

G

T

A

G

C

A

A

T

T

G

C

T

2

G

A

A

A

A

A

G

T

A

G

C

A

G

T

T

G

C

T

3

T

T

G

C

T

G

T

A

G

C

A

G

T

A

A

C

T

4

T

T

T

T

A

T

G

T

A

T

C

A

G

C

T

G

T

T

5

C

G

A

A

C

T

G

T

T

A

C

A

T

C

G

A

T

T

6

C

G

T

T

C

T

G

T

A

A

C

A

A

A

G

A

C

T

7

A

A

T

T

T

T

G

T

A

G

C

T

A

C

T

T

A

T

8

A

A

T

T

T

A

G

T

A

T

C

A

A

A

A

A

T

A

9

A

A

A

G

C

T

G

T

A

A

C

A

A

A

A

T

C

T

10

T

C

A

T

T

T

G

T

A

C

A

G

T

C

T

G

T

T

The numbers on the edges are the indexes of the array (starting with zero as usual).  We call out an item from the array by using two numbers in brackets: the row number, then the column number. If our array is called @sequences, then in the top row, $sequences[0][0] is "A", $sequences[0][1] is also "A", $sequence[0][6] is "G", and so forth.  Moving away from the top row, $sequences[8][12] is "A", and $sequences[9][6] if "G".

As with a one-dimensional array, one of the most straightforward things we can do is to print out the contents of an array. Here's a start:

foreach $row (0 .. scalar(@sequences) - 1) {
    print the contents of the row
}

foreach $row (0 .. scalar(@sequences) - 1) {
    foreach $column (something here about columns) {
        print $sequences[$row][$column];
    }
}

foreach $row (0 .. scalar(@sequences) - 1) {
    foreach $column (0 .. $sequence_length - 1) {
        print $sequences[$row][$column];
    }
}

If $sequence_length is not too big, we can add the linefeed at the end of each row:

foreach $row (0 .. scalar(@sequences) - 1) {
    foreach $column (0 .. $sequence_length - 1) {
        print $sequences[$row][$column];
    }
    print $LF;
}

The consensus.pl program has just this piece of code. Consensus.pl solves a problem that arose in Scenario 2. You might recall that the notes presented a table of NtcA-binding sites and then claimed that NtcA bound to sequences that looked like GTA........TAC. Where did THAT come from? Well, it came from crude, fuzzy impressions of the general features of the table. We can do better than that. And consensus.pl does.

The program calculates a consensus sequence by looking at each column of a table of sequences. If 80% of the bases are A, for instance, then the program will print a capital A in that column of the consensus sequence. If at least 50% of the bases in the column are A, then the program prints a lowercase a in that column. (Otherwise it prints a period.)  Download NtcA-binding.txt to try it out. (This file contains the NtcA-binding sequences from Scenario 2)

SQ2. In consensus.pl, why does the Calculate_consensus_sequence routine have $column in the outside for loop, and $row on the inside for loop, the opposite of the printing routine?

for $column (0 .. $sequence_length - 1) {
   @count = (0, 0, 0, 0);
   for $row (0 .. Size(@sequences) - 1) {
          . . .
   }
}

II. Homegrown BlastN

The BlastN.pl program (which you can test with the DG47 and lef sequences you got when going through the scenario) uses two dimensional arrays extensively, but its printing routines are rather complicated.  What it doesn't have, unfortunately, is a routine to print out two-dimensional arrays like the scoring matrix.  If we had such a routine, we might be able to watch BlastN as it calculated the scores, and so get a better idea of how it works.

SQ4. First of all, get BlastN.pl to run. Does it give you the same results as BlastN from NCBI? Take a look at the program and get a basic idea of how it works.

SQ5. Write a subroutine that will print out part of the scoring matrix. It should look something like this:

sub print_score {        
# prints out scoring matrix
# It's called by print_score(a,b,c,d)
# where a is assigned to $first_target
#       b is assigned to $last_target
#       c is assigned to $first_query
#       d is assigned to $last_query
# The table produced should look something like what's shown below
# (you don't have to print labels, just the numbers)

                #                 Query
                #        1st                     last
                # T  1st score score score  ...  score
                # a      score score score  ...  score
                # r      score score score  ...  score
                # g      score score score  ...  score
                # e       ...   ...   ...   ...   ...
                # t last score score score  ...  score

my ($first_target,$last_target,$first_query,$last_query) = @_;
   foreach $t (  CONTINUE THIS LINE
      foreach $q (  CONTINUE THIS LINE
         print  CONTINUE THIS LINE
      }
      print  CONTINUE THIS LINE
   }
}

• You'll probably want the numbers to line up.  One way to do that is by using the printf command instead of print.  If you say

printf "%6d", $n;

you'll print the number $n in a column six spaces wide.
 
• Don't forget that you need to call the subroutine before it does anything. You call it with a statement like:
 
print_score (Put four numbers or variables here, separated by commas );

SQ7. Play with BlastN, both the local and the NCBI varieties (use Blast 2 sequences for the latter), trying to characterize how the two implementations of the program differ. Consider, for example, filtering, scoring, and, of course, how their answers compare.

SQ8. Make changes in the parameters of the programs (e.g. the rewards and penalties). Do these changes affect the results?