Global alignment, affine gap model on Protein (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.

BLOSUM62 matrix, 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:
  -TTTTATGGTA
     |||| |||
  CACTTAT-GTA

Sequence 0 and 2:
  TTTTA-TGGTA-
   || | | ||
  -TTAACT-GTTT

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

Sequence 1 and 2:
  --CACT-TATGTA
     ||| | | |
  TTAACTGT-T-T-

Sequence 1 and 3:
  CACTTAT-G-T-A
  ||    | | | |
  CA---GTGGCTCA

Sequence 2 and 3:
  TTAACTGT---T-T
      | ||   |
  ----CAGTGGCTCA

Output:

0, 1: 31
0, 2: 26
0, 3: 23
1, 2: 27
1, 3: 27
2, 3: 17