How to extract the alignment sequence(progressiveMauve) from backbone file
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6.7 years ago
deepue ▴ 150

Hi,

I have aligned 5 bacterial genomes using the progressiveMauve. I would like to extract the part of the alignment having sequence in all the genome (eg: second and fourth line positions) using the alignment(.xmfa) file and backbone(.backbone) file.

seq0_leftend seq0_rightend seq1_leftend seq1_rightend seq2_leftend seq2_rightend seq3_leftend seq3_rightend seq4_leftend seq4_rightend
0 0 23127 23463 20107 20443 32207 32543 29528 29864
-28145 -28315 23464 23633 20444 20613 32544 32713 29865 30034
0 0 23634 23814 20614 20794 32714 32894 30035 30215
-27824 -28003 23815 23997 20795 20977 32895 33077 30216 30398


Is there any utility to achieve this task? How to extract only the lines having sequence from all the genomes(e.g., 2nd, 4th)?

Thanks.

mauve progressiveMauve genome backbone alignment • 2.5k views
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I think there was no better method to do it, and I suggest that you can try to extract the sequences using seqtk.