#38 GUI vs XMFA Text File

[Sarah]

Hello all,

I have aligned 2 whole genomes, one reference FASTA provided by NCBI and our own de novo assembled FASTA. When viewing the alignment on the GUI, we find a large insertion (~3000bp) at around 2.7Mb. When we pull the actual positions for this insertion from the text file, the insertion is at 3.7Mb. Why are these positions different? (see attachments for screenshots of both the text file and GUI) And which one should we consider as correct?

Any help is appreciated!

Thank you,

Sarah Ramirez-Busby
Biomedical and Medical Informatics
San Diego State University

[Aaron Darling]

Hi Sarah, the text screenshot does not appear to correspond to an XMFA file. Could that be from the .backbone or .bbcols file instead? If the numbers resulted from some processing of the XMFA data on your end, then I would suggest checking the code which processed the XMFA and/or posting that code here so we can better understand the issue.

[Sarah]

You're correct, the format of the text is output from a code I found in a
publication. The code pulls out information from the XMFA file. I used a
published code that parses the XMFA file and extracts indels. Code is
attached with corresponding publication.

We are needing positions of indels so if you have any suggestions as to how
to extract that from the XMFA file, we'd appreciate it. I found the code
searching through Google on what others have done to find indels.

Thanks for any help!

Sarah

Sarah Ramirez-Busby
Master's Candidate, Bioinformatics
San Diego State University
Valafar Lab, GMCS 403

On Thu, Jan 15, 2015 at 5:27 PM, Aaron Darling koadman@users.sf.net wrote:

Hi Sarah, the text screenshot does not appear to correspond to an XMFA
file. Could that be from the .backbone or .bbcols file instead? If the
numbers resulted from some processing of the XMFA data on your end, then I
would suggest checking the code which processed the XMFA and/or posting
that code here so we can better understand the issue.

---

• [bugs:#38] http://sourceforge.net/p/mauve/bugs/38 GUI vs XMFA Text
  File*

Status: open
Group: 2.1.0
Created: Thu Jan 15, 2015 10:15 PM UTC by Sarah
Last Updated: Thu Jan 15, 2015 10:15 PM UTC
Owner: nobody

Hello all,

I have aligned 2 whole genomes, one reference FASTA provided by NCBI and
our own de novo assembled FASTA. When viewing the alignment on the GUI, we
find a large insertion (~3000bp) at around 2.7Mb. When we pull the actual
positions for this insertion from the text file, the insertion is at 3.7Mb.
Why are these positions different? (see attachments for screenshots of both
the text file and GUI) And which one should we consider as correct?

Any help is appreciated!

Thank you,

Sarah Ramirez-Busby
Biomedical and Medical Informatics
San Diego State University

---

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[Aaron Darling]

Thanks Sarah, I'll check out that code.

In the meantime, I suggest you have a look at the .backbone file which progressiveMauve generates by default. It contains information on indels and I believe would serve your purpose.

[Sarah]

Hi Aaron,

I've been looking over the .backbone file (attached) but I'm seeing
negative numbers in the first sequence (our de novo assembled genome). I'm
not sure how to interpret these.

Two questions:

Lines 5-7 in sequence 0 would be considered deleted from sequence 1 or were
inserted into sequence 0?
Line 8 deleted from sequence 0 or inserted into sequence 1?

Thank you for your help!

Sarah

Sarah Ramirez-Busby
Master's Candidate, Bioinformatics
San Diego State University
Valafar Lab, GMCS 403

On Thu, Jan 15, 2015 at 6:29 PM, Aaron Darling koadman@users.sf.net wrote:

Thanks Sarah, I'll check out that code.

In the meantime, I suggest you have a look at the .backbone file which
progressiveMauve generates by default. It contains information on indels
and I believe would serve your purpose.

---

• [bugs:#38] http://sourceforge.net/p/mauve/bugs/38 GUI vs XMFA Text
  File*

Status: open
Group: 2.1.0
Created: Thu Jan 15, 2015 10:15 PM UTC by Sarah
Last Updated: Fri Jan 16, 2015 01:27 AM UTC
Owner: nobody

Hello all,

I have aligned 2 whole genomes, one reference FASTA provided by NCBI and
our own de novo assembled FASTA. When viewing the alignment on the GUI, we
find a large insertion (~3000bp) at around 2.7Mb. When we pull the actual
positions for this insertion from the text file, the insertion is at 3.7Mb.
Why are these positions different? (see attachments for screenshots of both
the text file and GUI) And which one should we consider as correct?

Any help is appreciated!

Thank you,

Sarah Ramirez-Busby
Biomedical and Medical Informatics
San Diego State University

---

Sent from sourceforge.net because you indicated interest in
https://sourceforge.net/p/mauve/bugs/38/

To unsubscribe from further messages, please visit
https://sourceforge.net/auth/subscriptions/

[Aaron Darling]

Hi Sarah, your attachment didn't show up. I would suggest reading this page to understand the format of the file, meaning of negative numbers, etc:
http://darlinglab.org/mauve/user-guide/files.html

See the section entitled "The Progressive Mauve backbone file"