Local alignment, affine gap model on DNA (Pairwise Alignment)

• Category: Pairwise Alignment
• Validator: Pairwise Alignment Validator

Description

Given 2000 reads of length 100, compute the local 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:
  TTATGGTA
  |||| |||
  TTAT-GTA

Sequence 0 and 2:
  TT-A-TGGT
  || | | ||
  TTAACT-GT

Sequence 0 and 3:
  A-TGG-T-A
  | ||| | |
  AGTGGCTCA

Sequence 1 and 2:
  TT-A-TGT
  || | |||
  TTAACTGT

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

Sequence 2 and 3:
  CT
  ||
  CT

Output:

0, 1: 13
0, 2: 9
0, 3: 9
1, 2: 10
1, 3: 6
2, 3: 4