Sequence alignment

Below is shown a dump of the four matrices used to make the sequence alignment of two fasta files. You can use this to compare the output from you fasta_align_O3 and fasta_align program. The output was made aligning two small fasta files q1.fsa and q2.fsa.

First copy these two fasta files to your data directory

cd $ALGOHOME/data
cp /usr/opt/www/pub/CBS/courses/27625.algo/exercises/data/Align/q?.fsa .

Next run the command

fasta_align_O3 -show -gf 2 -gn 1 q1.fsa q2.fsa

The output to the screen should look like

# Gap penalties. fgap: 2.000000. ngap: 1.000000
# S-matrix
   V    L    L    P    V    L    L    P 
V 41.00 39.00 36.00 30.00 20.00 16.00 13.00  7.00  0.00
L 35.00 36.00 38.00 31.00 20.00 15.00 15.00  8.00  0.00
P 29.00 30.00 31.00 33.00 21.00 15.00 10.00 10.00  0.00
V 24.00 21.00 20.00 21.00 23.00 16.00 11.00  5.00  0.00
L 18.00 19.00 20.00 16.00 18.00 18.00 12.00  6.00  0.00
I 17.00 17.00 14.00 15.00 17.00 17.00 13.00  7.00  0.00
L 12.00 13.00 15.00 11.00 12.00 13.00 15.00  8.00  0.00
P  6.00  7.00  8.00 10.00  6.00  7.00  8.00 10.00  0.00
   0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00
# Eij-matrix
   V    L    L    P    V    L    L    P 
V  1  1  2  3  1  1  2  3  0
L  5  1  1  2  3  1  1  2  0
P  5  5  4  1  2  3  3  1  0
V  1  1  5  4  1  2  3  3  0
L  1  1  1  4  1  1  1  3  0
I  1  1  5  4  1  1  2  3  0
L  5  1  1  5  5  1  1  2  0
P  5  5  4  1  5  5  4  1  0
   0  0  0  0  0  0  0  0  0
ALN Q2 8 Q1 8 type SW_ALN alen 9 7 7 2 score 41 -99.9 -41 -99.900002
QAL Q2     0 VL-PVLILP
DAL Q1     0 VLLPVL-LP

Next you can do the same for the fasta_align program

fasta_align -show -gf 2 -gn 1 q1.fsa q2.fsa

The output to the screen should look like

# S-matrix
   V    L    L    P    V    L    L    P 
V 41.00 39.00 36.00 30.00 20.00 16.00 13.00  7.00  0.00
L 35.00 36.00 38.00 31.00 20.00 15.00 15.00  8.00  0.00
P 29.00 30.00 31.00 33.00 21.00 15.00 10.00 10.00  0.00
V 24.00 21.00 20.00 21.00 23.00 16.00 11.00  5.00  0.00
L 18.00 19.00 20.00 16.00 18.00 18.00 12.00  6.00  0.00
I 17.00 17.00 14.00 15.00 17.00 17.00 13.00  7.00  0.00
L 12.00 13.00 15.00 11.00 12.00 13.00 15.00  8.00  0.00
P  6.00  7.00  8.00 10.00  6.00  7.00  8.00 10.00  0.00
   0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00
# Q-matrix
   V    L    L    P    V    L    L    P 
V 33.00 34.00 36.00 30.00 19.00 13.00 13.00  7.00  0.00
L 27.00 28.00 29.00 31.00 20.00 14.00  9.00  8.00  0.00
P 22.00 19.00 18.00 19.00 21.00 15.00 10.00  4.00  0.00
V 16.00 17.00 18.00 14.00 16.00 16.00 11.00  5.00  0.00
L 15.00 15.00 12.00 13.00 15.00 15.00 12.00  6.00  0.00
I 10.00 11.00 13.00  9.00 10.00 11.00 13.00  7.00  0.00
L  4.00  5.00  6.00  8.00  4.00  5.00  6.00  8.00  0.00
P -1.00 -1.00 -1.00 -1.00 -1.00 -1.00 -1.00 -1.00  0.00
   0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00
# P-matrix
   V    L    L    P    V    L    L    P 
V 37.00 34.00 28.00 18.00 14.00 11.00  5.00 -1.00  0.00
L 35.00 36.00 29.00 18.00 13.00 13.00  6.00 -1.00  0.00
P 29.00 30.00 31.00 19.00 13.00  8.00  8.00 -1.00  0.00
V 19.00 19.00 20.00 21.00 14.00  9.00  3.00 -1.00  0.00
L 17.00 18.00 15.00 16.00 16.00 10.00  4.00 -1.00  0.00
I 15.00 13.00 14.00 15.00 15.00 11.00  5.00 -1.00  0.00
L 12.00 13.00 10.00 11.00 12.00 13.00  6.00 -1.00  0.00
P  6.00  7.00  8.00  5.00  6.00  7.00  8.00 -1.00  0.00
   0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00
# Eij-matrix
   V    L    L    P    V    L    L    P 
V  1  1  2  3  1  1  2  3  0
L  5  1  1  2  3  1  1  2  0
P  5  5  4  1  2  3  3  1  0
V  1  1  5  4  1  2  3  3  0
L  1  1  1  4  1  1  1  3  0
I  1  1  5  4  1  1  2  3  0
L  5  1  1  5  5  1  1  2  0
P  5  5  4  1  5  5  4  1  0
   0  0  0  0  0  0  0  0  0
ALN Q2 8 Q1 8 type SW_ALN alen 9 7 7 2 score 41 -99.9 -41 -99.900002
QAL Q2     0 VL-PVLILP
DAL Q1     0 VLLPVL-LP