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Sequence alignmentBelow 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 |