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Recent Activity
All posts created by debbie
Link to this post | posted 26 Jun, 2018 21:14 | |
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Germán, Excellent obse4rvaton of the data! -debbie |
Posted in: Frameshifts and Introns → New frameshift in an A1 phage?
Link to this post | posted 22 Jun, 2018 17:17 | |
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Hi. I sent an email to Dex and Claire about this. Technically, we are not reporting codon or anti-codon but rather the DNA sequence that makes the anti-codon. So I can see why this gets confusing. |
Posted in: PECAAN → PECAAN and tRNA notes problem?
Link to this post | posted 21 Jun, 2018 21:56 | |
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Evan, GeneMark does call all starts ATG, GTG, and TTG (you will find that GenMark can agree with Glimmer on a TTG start in DNA Master). However, GeneMrk's graphic output is only coded to represent ATG (longer upticks) and TTG (shorter upticks) starts. I think they ran out of money to update all of the graphic displays….. |
Link to this post | posted 21 Jun, 2018 16:24 | |
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Check out the genes upstream of the tail assembly chaperone (in Adaia, they are genes 8 and 9). it is easy to see that gene 8 is the major tail (HHPred results). Remember that it matches the SPP1 crystal structure project. This gene matches "H" which is a major tail protein and NOT the portal or head-to-tail connector complex protein. I am wondering if there is a legitimate programmed frameshift with this protein. See Baranov, et al 2006 where a major tail +1 ribosomal slippage is cited in a Listeria phage, PSA. While our slippery sequence doesn't match the one found in that major tail protein, our major tail protein - gp 8 - is 140 amino acids, while gp9 is 130 amino acids. A quick look at other major tail proteins across the actinobacteriophages, I have found gp sizes of 170 - 282 amino acids. Just wondering if the major tail protein is in 2 genes in this case. Further review is needed. |
Posted in: Cluster AX Annotation Tips → Major Tail Proteins
Link to this post | posted 21 Jun, 2018 16:10 | |
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Be careful as you look for the second part of the tail assembly chaperone (T protein). It is a tiny bit of coding potential directly upstream of the tape measure that is not always called (only 1 in 3 have predicted it so far). All of them have same slippery sequence. refer to genome annotations of Adaia, Sputnik, and Atraxa for the exact calls. |
Posted in: Cluster AX Annotation Tips → Tail Assembly Chaperones
Link to this post | posted 15 Jun, 2018 15:00 | |
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So you may be missing a driver. I am not sure. I have attached a picture of 3 files that should be in your DNA Master folder. Check the root of where these files are (captured in the attached photo) along with the 3 files that should be there. They are Windows files and don't move easily. I am providing one of them becuase it is the one that is usually missing. If you can't access this file from my DropBox, download it from the web. https://www.dropbox.com/s/uzlq44kn958fyma/msvcr100.dll?dl=0 |
Posted in: DNA Master → Important DNA Master Update
Link to this post | posted 14 Jun, 2018 21:19 | |
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The version is at help -> about. If you have not changed preferences to use secure servers, you will not get blast results. I have attached a picture of the correct settings. |
Posted in: DNA Master → Important DNA Master Update
Link to this post | posted 13 Jun, 2018 12:39 | |
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Rick, This post should get your DNA master updated. debbie Dan Russell |
Posted in: DNA Master → Important DNA Master Update
Link to this post | posted 06 Jun, 2018 21:01 | |
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I think that the functional call for this particular instance could be nuclease. |
Posted in: Request a new function on the SEA-PHAGES official list → DNA double-strand break repair protein
Link to this post | posted 03 Jun, 2018 20:09 | |
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I think that we have missed a gene in these genomes. Look at the gap between upstream of the tape measure. I don't (yet) see the slippery sequence, but I think that is the T region of the G-T protein of a tail assembly chaperone. |
Posted in: Cluster AN Annotation Tips → tail assembly chaperone