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Genome Comparison

| posted 11 Mar, 2019 16:34
Hi,
I am trying to make a genome comparison to calculate the ANI values, but when I run the analyses DNA Master shows a warning message "pair analysis exception".
Could someone please help me with this error??

Thanks in advance

Cristian
| posted 11 Mar, 2019 19:07
cristian,
I have my students use this online tool for ANI calculations, sorry it doesn't answer your question but a work around is better than nothing:

http://enve-omics.ce.gatech.edu/ani/
| posted 11 Mar, 2019 19:22
Christian,

We use that one as well, and also OrthoANI, here:
https://www.ezbiocloud.net/tools
https://www.ezbiocloud.net/tools/ani
Steve
| posted 11 Mar, 2019 21:51
Thanks cdshaffer and Steven,
I need to compare 80 genomes all-vs-all to build a double entry matriz with the ANI values.
Do you know if these programs are suitable for this task?
Thanks!!

Cristian.-
| posted 11 Mar, 2019 22:40
I know you can run OrthoANI as a stand alone program and do so. I let Ivan do that, though, since it's command line. The GUI based one has a limit of 10 genomes. It didn't seem to be particularly challenging for him. Might give him a shout if you run into any trouble.

Steve
| posted 13 Mar, 2019 11:21
Thank you very much Steven. I ran the stand alone version of OrthoANI without any problem. The only thing is that some value of ANI was -1.0 (negative).Do you know what could be the reason?
Thank you again
| posted 13 Mar, 2019 16:24
I don't know. I wouldn't be surprised it that wasn't an error code or below the measurable threshold code, but I don't know offhand, I'm afraid.
| posted 13 Mar, 2019 16:34
Hi Cristian,
I've never seen the error that you are describing, but I can tell you that I've had difficulty performing simultaneous comparisons with 80 phages. I had to do it in smaller chunks (like 20 at a time) and then collect the answers in a spreadsheet. So it is possible you are maxing it out.

Best,
Welkin
| posted 13 Mar, 2019 18:54
Thanks Steven and Welkin,
I have tried to compare with a set of 20 phages and the negative values was still there. Then I ran the online version of the program with the sequences of two phages with -1.0% ANI and the result was the same. I don`t know what is the problem with these phages..

Thanks!

Cristian.-
 
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