Link to this post | posted 08 Feb, 2018 02:08
delesall	Yes I did look at Xu, Hendrix and Duda - I don't see any of the slippery sequences they identify in these phages (at least in the region where I expect frameshift to occur). So I am still perplexed but isn't that the pleasure of phage annotation? :-) Veronique

Link to this post | posted 06 Feb, 2018 18:44

delesall

I'm looking at the tail assembly chaperones of a Gordonia CZ1 phage, Eviarto. Four other CZ1 phages have been annotated but I don't see why the frameshift was called the way it was. Two issues: 1) the frameshift in Nymphadora gp 14 and 15 was called at a different place from that in BatStarr, Kita, and Zirinka (see attached document). 2) the sequences were the frameshift is called don't look slippery to me (in Nymphadora (AAGCG; in others CAGGC) and don't look like the ones identified in Xu et al. What am I missing? I do see a region - CCCGAAA - just before the "called" frameshift for Nymphadora that looks slippery to me (starting at bp 9880 in Eviarto)… Any advice? 13Kb

Link to this post | posted 04 Feb, 2018 19:08

delesall

First, sharing/repeating instructions from Welkin "We have been reviewing our functional assignments for the head-to-tail connector proteins due to some feedback we've received from a reviewer. We've decided to proceed in two ways: 1) We will not use the functional assignment "head-to-tail connector" anymore. Instead we will be switching to "head-to-tail connector complex protein". 2) Only genes that have HHPred alignments to crystal structures (so must be a PDB hit) to a known connector complex protein can be assigned this function. This includes phage SPP1 genes 15 and 16; phage HK97 gene 6, and Bacillus protein yqbG." So, I'm looking at Gordonia phage Eviarto (CZ1), I've got HHPred alignments with PDB support for genes 8 and 9, but not PDB support for gene 10. However, that gene has nice matches to minor capsid protein. So, call minor capsid?

Link to this post | posted 03 Feb, 2018 17:05
delesall	I have a student who cannot update DNAMaster on her Mac. Every time she updates and reopens, the update has not "taken". Any suggestions? Thx

Link to this post | posted 29 Jan, 2018 19:00
delesall	Unless I missed it, there is no Gordonia terrae in GeneMark list but there is a Gordonia species. Have people used the GeneMark output trained on this Gordonia species? Is it better to use the heuristic GeneMark only or both outputs? Cheers, Veronique Edited 21 Feb, 2018 16:13

Link to this post | posted 12 Jan, 2018 17:50

delesall

Evan Merkhofer Veronique Delesalle Figure it out! Completely forgot to update before doing auto-annotation! What a dunce! But if somebody does have a document with things to know about running DNAMaster on a mac, I still would love that. :-) I'm having the same issue, and I have updated the version of WINE. I'm running version 5.23.2, Build 2537, updated Dec. 11, 2017. When I auto-annotate, I get no features in my file. Has anyone else had this problem?' Evan After you updated, did you change the Gene Prediction and Secure Connection "preferences"? See the DNAMaster_Update document of September 2017. Veronique

Link to this post | posted 11 Jan, 2018 19:13
delesall	Figure it out! Completely forgot to update before doing auto-annotation! What a dunce! But if somebody does have a document with things to know about running DNAMaster on a mac, I still would love that. :-)

Link to this post | posted 11 Jan, 2018 18:33

delesall

Hi all I just downloaded DNAMaster from the Baylor site (https://baylor.app.box.com/v/DNAMasterMac) using the version from 2017.5.23 I have been able to upload a sequence but when I do an auto-annotation (no blasting) nothing appears in the features? Any advice? And has somebody compiled a document on issues and things to know about running DNAMaster on a mac and is willing to share? Thanks and happy annotating in 2018! Veronique

Link to this post | posted 11 Aug, 2017 21:27
delesall	So, I should have better phrased my question. Do we want the prob of a CCM to be greater than 0 or greater than as certain value? If so, what is that threshold? prob of 0.2 or 0.5?

Link to this post | posted 11 Aug, 2017 03:34

delesall

The Lysin A in Gordonia phage is encoded by two genes, representing two domains. In Gordonia phage Adgers, these two genes correspond to N-acetyl-BetaD-muramidase domain (pfam 01510) and to a peptidase domain (pfam 01551). In Gordonia phage SuperSulley, the two Lysin A genes are ORF 49 (start 37820) and ORF 50 (start 38485) and respectively correspond to a peptidase domain (pfam 13529) and to a glycoside hydrolase (cd00325). See Payne and Hatfull (2012 PlosOne - Mycobactteriophage Endolysins…. pfam 13529 is not listed in Table 1!