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Recent Activity
All posts created by debbie
| Link to this post | posted 26 May, 2021 21:34 | |
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Joe, We do not use function field. We record function in the product field and you can auto-populate the fields of your choice by using the arrow that is in the upper right corner of each field. Make sense? debbie |
Posted in: DNA Master → Function field
| Link to this post | posted 26 May, 2021 01:46 | |
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Hi Kathleen, Sounds like your preferences are not quite right. https://seaphagesbioinformatics.helpdocsonline.com/article-66 In step 2, make sure that you have the server set correctly. the unlock code is Hatfull and there is no password. debbie |
Posted in: DNA Master → Important DNA Master Update
| Link to this post | posted 25 May, 2021 17:28 | |
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Hi Nikki, I am sure I called CrystalP, and now want to disagree with the intron part of that call. According to the literature, the introns have to be self-splicing in a prokaryote. So it has to be ~200-ish nucleotides. As for whether that second tRNA is worth calling, the argument has persisted for 17 years. I need to investigate further. Give me a bit of time for this one. thanks, debbie |
Posted in: tRNAs → short introns in tRNAs in cluster E
| Link to this post | posted 25 May, 2021 16:58 | |
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Hurray! |
Posted in: DNA Master → BLAST won't save
| Link to this post | posted 24 May, 2021 20:08 | |
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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. |
49KbPosted in: DNA Master → DNA master server down?
| Link to this post | posted 24 May, 2021 14:13 | |
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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 |
Posted in: DNA Master → BLAST won't save
| Link to this post | posted 20 May, 2021 19:52 | |
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It does now. Sorry about the  snafu! i am getting notices every time you try to fix it.
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Posted in: Request a new function on the SEA-PHAGES official list → antitoxin in toxin/antitoxin system, BrnA-like
| Link to this post | posted 07 May, 2021 20:42 | |
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You too! Terrific that you contacted Kirk! Thanks, debbie |
| Link to this post | posted 07 May, 2021 20:03 | |
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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 | |
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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 |