Re: [Mauve-users] How to extract the alignment sequence

[Susan B. F. <fo...@ug...>]

Hi Gopi,

If you go to the link I gave you, the attachment is at the top of the first posting from Lu Cheng.  It is a very small font and blue.

-S

From: Gopi Nath [mailto:its...@gm...]
Sent: Tuesday, February 09, 2016 4:50 AM
To: Susan Beth Fogelson
Cc: mau...@li...
Subject: Re: [Mauve-users] How to extract the alignment sequence

Hi Susan,

Thank you for the information.

I have been trying to look at the xmfa2fasta.pl<http://xmfa2fasta.pl> script mentioned in the third step, but unfortunately it is not available.

Do you have any idea if it has been to some other location ?

On Wed, Feb 3, 2016 at 9:12 PM, Susan Beth Fogelson <fo...@ug...<mailto:fo...@ug...>> wrote:
Hi Gopi,

If I understand you correctly, you are trying to extract the LCBs from your alignments. I used the stripsubsetsLCB command to do this with the genomes I am working with.  The only issue I had was that if you ran your alignment in the Windows GUI and not using Linux then the path names won’t recognize the input files.  Below is the link to the linux commands that I used. Hope this is helpful.

http://sourceforge.net/p/mauve/mailman/mauve-users/thread/51F...@he.../


-Susan

From: Gopi Nath [mailto:its...@gm...<mailto:its...@gm...>]
Sent: Wednesday, February 03, 2016 1:58 PM
To: mau...@li...<mailto:mau...@li...>
Subject: [Mauve-users] How to extract the alignment sequence

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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