Link to this post | posted 24 May, 2021 20:08
debbie	Kathleen, I just tried. My mac asked me to choose an application to open the ftp link. I clicked the "always" box and it downloaded. (see message screen shot). I did not overtly select an application. 49Kb

Link to this post | posted 24 May, 2021 14:13

debbie

Nikki, I have not encountered that. Here are some thoughts about it. what is the size of the blasted file. Is it the size of a blasted or unblasted file (meaning is it 50kb or 250 kb-ish?) If it is bigger, then the blast date is there. I am guessing that if you unpack and repack the .dnam5 file, it will 'appear". https://seaphagesbioinformatics.helpdocsonline.com/article-104 what you will have do differently is go into the blast folder to make sure you have all the files. Not sure it is the problem, but worth looking in to. debbie

Link to this post | posted 20 May, 2021 19:52
debbie	It does now. Sorry about the snafu! i am getting notices every time you try to fix it.

Link to this post | posted 07 May, 2021 20:42
debbie	You too! Terrific that you contacted Kirk! Thanks, debbie

Link to this post | posted 07 May, 2021 20:03
debbie	Hi Andrea, i do not know how to do this in PECAAN, but in following Kirk's explanation for Coco12, i would annotate it the same way he did. debbie

Link to this post | posted 07 May, 2021 19:23
debbie	Hi Kristen and all, This is one of those genes that needs a dig deep. Here are some of what i have been thinking. I am reluctant to call a RecE without a RecT. I don't know how to differentiate between a RecE, a generic exonuclease or the Cas4 family exonuclease. I am looking forward to what we can figure out about these. Good question, sorry to not be of much help. debbie

Link to this post | posted 05 May, 2021 01:02
debbie	I would delete this gene because we don't believe that 2 genes exist in the same space of a genome. Genes can overlap a bit, but this is completely covered by the forward genes 35 and 37. they are better choices because it is unlikely that a gene would be in the opposite direction 'for no good reason'. What do you think? debbie

Link to this post | posted 04 May, 2021 20:47

debbie

Becky, I wrote this way before Chris posted. So to muddle this a bit. Hi. I think I would like to call this O-acetyltransferase A. I have attached an article that describes this gene as having 2 domains, which I believe I see in LonelyBoi_31, namely an acetyltransferase and a SGNH hydrolase fold. Let me know what you think, debbie https://www.sciencedirect.com/science/article/pii/S0021925817494105?via%3Dihub Edited 04 May, 2021 20:48

Link to this post | posted 04 May, 2021 19:59

debbie

Hi folks, I need more info. What is the relationship with the upstream and downstream gene in this genome? Cluster F genomes are chucked full of tiny genes that have the 4 bp overlap with each other. If this gene has that I would call it. Also blastn the sequence to see if this is more highly conserved. If it is, does that influence your call? Looking forward to what you are thinking? Send the .dnam5 file is you want me to look further. Thanks, debbie

Link to this post | posted 03 May, 2021 12:56
debbie	Hi, I would use this terminology: RepA-like replication initiator What do you think? debbie