Global alignment, linear gap model on DNA (Pairwise Alignment)

• Category: Pairwise Alignment
• Validator: Pairwise Alignment Validator

Description

Given 2000 reads of length 100, compute the global alignment using the linear gap model of all pairs.

Match: 2, mismatch: -3, gap: -2.

Input

• 2000 reads of length 100 (i.e., data/genome.pairwise_alignment.reads.length.100.fa)

Output

For each pair of sequences, output the score of the alignment.

The output must be written into a file.

Example

For simplicity we assume 4 reads of length 10.

Reads:

> 1
TTTTATGGTA
> 2
CACTTATGTA
> 3
TTAACTGTTT
> 4
CAGTGGCTCA

Resulting alignments:

Sequence 0 and 1:
  -TTTTATGGTA
     |||| |||
  CACTTAT-GTA

Sequence 0 and 2:
  TTTTA-TGGTA
   || | || |
  -TTAACTGTTT

Sequence 0 and 3:
  TTTTA-TGG-T-A
      | ||| | |
  ---CAGTGGCTCA

Sequence 1 and 2:
  CACTT-A-TG-TA
     || | || |
  ---TTAACTGTTT

Sequence 1 and 3:
  CACTTATG-T-A
  ||  |  | | |
  CA-GT-GGCTCA

Sequence 2 and 3:
  TTAACT-G-TTT
     | | | |
  --CAGTGGCTCA

Output:

0, 1: 4
0, 2: -1
0, 3: -3
1, 2: -3
1, 3: -2
2, 3: -12