Global alignment, affine 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 affine gap model of all pairs.

Match: 2, mismatch: -3, gap_extend: -3, gap_open: -1.

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:
  TT---TTATGGTA
       |||| |||
  --CACTTAT-GTA

Sequence 0 and 2:
  TTTT-A-TGGTA--
    || | | ||
  --TTAACT-GT-TT

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

Sequence 1 and 2:
  CACTT-A-TGTA--
     || | |||
  ---TTAACTGT-TT

Sequence 1 and 3:
  CACTTA-T-G-T-A
    |  | | | | |
  --C--AGTGGCTCA

Sequence 2 and 3:
  TTAACT-GTT---T--
      |  | |   |
  ----C-AG-TGGCTCA

Output:

0, 1: 8
0, 2: 4
0, 3: 4
1, 2: 4
1, 3: 4
2, 3: -4