SEA-PHAGES | DNAmaster

Link to this post \| posted today, 01:17
dstarkey	Hello, I am trying to run DNAmaster virtually on a MAC for the first time. I was able to get the program running and download my fasta file. However, the fasta file is to short (by 1 bp) and I receive the following error message when I try to work with the data (see attached). I'm looking for suggestions as what I am doing wrong and how I may fix the issue. Thanks, Dave Starkey 275Kb

Link to this post \| posted today, 16:54
debbie	Hi Dave, This is not typically something that occurs in DNA Master. So my first question is how did you download the fasta file. Did you open it? Download it again, without opening it and open it in DNA Master using Open -> FastA Multiple Sequence file. Is the sequence length now 50451? Let me know and we can go from there. best, debbie

Link to this post \| posted today, 17:38
dstarkey	Debbie, We are trying to run DNAmaster through a virtual PC environment on a MAC with an M1 chip. So I used the virtual PC's chrome browser to go to the Sea-Phages website. Once there, I used the search function to find our phage (bugatti) and downloaded the fasta file - it was put in virtual PC downloads. Then, I went into DNAmaster and used the open fasta multiple sequence file option to download the sequence into DNAmaster. When the program opened the file, the DNA sequence was there, but it was 50540bp not the stated 50541bp. I retried (3x) and each time the file was of the same length i.e., 1bp short. My students and I are getting frustrated that we cant get the program to work. And as we are already in week 2, we are feeling behind in the annotation process. The most practical solution might be to buy a PC and running the program that way. Thanks for you input and help, Dave

Link to this post | posted today, 17:38

dstarkey

Debbie,
We are trying to run DNAmaster through a virtual PC environment on a MAC with an M1 chip. So I used the virtual PC's chrome browser to go to the Sea-Phages website. Once there, I used the search function to find our phage (bugatti) and downloaded the fasta file - it was put in virtual PC downloads. Then, I went into DNAmaster and used the open fasta multiple sequence file option to download the sequence into DNAmaster. When the program opened the file, the DNA sequence was there, but it was 50540bp not the stated 50541bp. I retried (3x) and each time the file was of the same length i.e., 1bp short. My students and I are getting frustrated that we cant get the program to work. And as we are already in week 2, we are feeling behind in the annotation process. The most practical solution might be to buy a PC and running the program that way.
Thanks for you input and help,
Dave

Link to this post \| posted today, 17:58
debbie	Dave, Did you attend or watch Friday's Faculty Meeting? that might help you approach. https://seaphages.org/forums/topic/5861/ So it sounds like you did not open the file in anyway, but when DNA Master did, it had 1 less base. (I too run DNA Master on a virtual PC environment (Virtual Box) and have not encountered this. anyways… There is one other thing that you can try. After you open it in DNA Master, Export "Create Sequence from this entry only". click over to sequence and click "Raw". Did the sequence length change? Additionally, put the Bugatti.fasta file on the Desktop of your virtual machine. then Open it in DNAMaster from there. Very strange. I have auto-annotated Bugatti. See if this one is correct. Best, debbie 293Kb

Link to this post | posted today, 17:58

debbie

Dave,
Did you attend or watch Friday's Faculty Meeting? that might help you approach.
https://seaphages.org/forums/topic/5861/

So it sounds like you did not open the file in anyway, but when DNA Master did, it had 1 less base. (I too run DNA Master on a virtual PC environment (Virtual Box) and have not encountered this. anyways…
There is one other thing that you can try.
After you open it in DNA Master, Export "Create Sequence from this entry only". click over to sequence and click "Raw". Did the sequence length change?

Additionally, put the Bugatti.fasta file on the Desktop of your virtual machine. then Open it in DNAMaster from there.

Very strange.

I have auto-annotated Bugatti. See if this one is correct.

Best,
debbie

Link to this post \| posted today, 17:59
debbie	DNA Master file. 30Kb

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