Link to this post | posted 06 Aug, 2018 16:27
debbie	Sally, Hi. Using web Phamerator's gene numbers, I would call gene 16 a TAC. Neither 15 or 18 are good candidates by HHpred (gp 15 is a ribosomal protein hit) and 18 has no significant matches). I believe that gp 16 is also a TAC, BUT I would not call it. I can't find a slippery sequence and the Pfam hit is too weak for me.

Link to this post | posted 25 Jul, 2018 16:37

debbie

I am not sure exactly how to answer this without seeing data. Know that we made a decision about 1 1/2 years ago, to call every small gene between the major capsid and the major tail a -head-to-tail connector protein. Those calls should be ignored without HHPred info. If your BLAST hits our phages, you should be able to tell the difference because when we were calling 'everything', the label was "head-to-tail connector". Once we made the change we are labeling true hits to head-to-tail proteins "head-to-tail connector complex proteins". I hope that helps. it is a bit confusing. debbie

Link to this post | posted 24 Jul, 2018 03:49
debbie	The last feature of this genome is not in phamerator or in the gene list on phagesDB: CDS join(16287..16604,1..96) /gene="25" /locus_tag="PBI_EMPEROR_25" /codon_start=1 /transl_table=11 /product="HNH endonuclease" /translation="MTALPAWAGDYSRRLTALCLATYGDTCHLCGRPGATTADHLIPR SVSYDDSLANLRPAHQRCNSARGAMPIETWRARFTASTAPRSSRWSRPSSSLTPQVSA ALRPAAFFSPNAQNKGSVHTEKPSETTKGPDNATT"

Link to this post | posted 22 Jul, 2018 02:35
debbie	Maria, I would call both of these. They meet the cut-off criteria that we have set forth. for Neferthena, it looks like the end are called correctly. For Andromedas, you will need to trim the last 2 bases (GA). debbie Edited 22 Jul, 2018 10:54

Link to this post | posted 26 Jun, 2018 21:14
debbie	Germán, Excellent obse4rvaton of the data! -debbie

Link to this post | posted 22 Jun, 2018 17:17
debbie	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. Edited 22 Jun, 2018 19:42

Link to this post | posted 21 Jun, 2018 21:56
debbie	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

debbie

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. Edited 21 Jun, 2018 16:27

Link to this post | posted 21 Jun, 2018 16:10
debbie	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.

Link to this post | posted 15 Jun, 2018 15:00

debbie

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 37Kb