Question: How to extract the alignment sequence(progressiveMauve) from backbone file
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gravatar for deepue
2.9 years ago by
deepue110
Finland
deepue110 wrote:

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(eg: 2nd, 4th) ?

Thanks.

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