Link to this post | posted yesterday, 19:34

debbie

Hi Allison, In general, I would discourage using Blastp at ncbi for stat information. My rationale is this. Do not use any Ref Sequence data because it is not provided by the owner of the sequence. For most data outside of the SEA-PHAGES program annotations are done with automated software and does not follow the same scrutiny that we use. Finally having Starterator data (with 'raw' nucleotide alignments) surpasses alignments provided of called genes that have not gone though our scrutiny. As for the clustering part, again that is provided in Starterator. Also, matches to identical sequences doesn't provide much depth either. You are looking at same instances when they are identical, in which case whether you agree or not is a about whether 'we' agree' with each other, not how a sequence is conserved over time. The hits to non-actinobacteriophage data is of interest, but again what criteria was used to make that call, especially as it pertains to starts. There is some really nice data available at the ncbi hits that could also be investigated. LIke multiple seqeunce alignments. best, debbie

Link to this post | posted 23 Jan, 2026 19:48

debbie

Hi Holly, The use of membrane protein has a long history, but currrently, it is not being posted at phagesDB. Instead the data is always available at phamerator.org in the drop down box of each gene and a button selection that shows all membrane proteins in the Genome Map Settings. However, this function is part of the GenBank file and PLEASE include them in your annotations. Best, debbie The historical perspective is that membrane protein (domain) is NOT a function, BUT knowing a gene has a membrane domain may help to identify function is surrounding genes. Hence, the data at Phamerator.org is most helpful! debbie

Link to this post | posted 22 Jan, 2026 19:00
debbie	that is ok with me. best, debbie

Link to this post | posted 22 Jan, 2026 17:59
debbie	Dave, It might be helpful to meet up on line and you can show me what is happening. Tomorrow would be better than today. best, debbie

Link to this post | posted 22 Jan, 2026 12:16
debbie	Dave, You have to be signed into too seaphages.org to access. (It is the same as phagesDB). Did you see my file? debbie

Link to this post | posted 21 Jan, 2026 17:59
debbie	DNA Master file. 30Kb

Link to this post | posted 21 Jan, 2026 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 21 Jan, 2026 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 13 Jan, 2026 18:01
debbie	Hi Dave. I am on a Mac and I use Virtual Box, with Windows 11. debbie

Link to this post | posted 08 Jan, 2026 01:12

debbie

Hi Beth, I'm finally answering this here also. Sorry for the delay. The original University of Pittsburgh server that housed DNA Master is no longer available. User the directions in the Genomics guide, section 2.5 to get DNA master installed. do not use any previous directions. And do not auto-install. Change the location of installation as described in the guide. And for those of you who are struggling with this installation. DNA Master provides information that is essential for a good annotation. IN a classroom setting, pair up your students, then you only need 1/2 as many computers loaded with this software! there is plaenty of work to do with the other programs. Best, debbie