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All posts created by delesall

| posted 21 Feb, 2018 18:35
OK - We will do some more comparative investigations and I will update then!
Posted in: Frameshifts and IntronsCZ1 Tail assembly proteins
| posted 09 Feb, 2018 20:14
So in Eviarto, as mentioned above, I see a region that looks slippery around bp 9875 to 9886. I also see a region of 5 G starting at 9752. I don't see any stop codons that would make frameshifting at these sites not possible…
Posted in: Frameshifts and IntronsCZ1 Tail assembly proteins
| posted 08 Feb, 2018 20:29
Yes - the word from Pitt is that we need crystal structures data to call the HT connector complex protein. This is a change from what we did previously.
Posted in: Functional AnnotationHead-tail connectors
| posted 08 Feb, 2018 02:08
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
Posted in: Frameshifts and IntronsCZ1 Tail assembly proteins
| posted 06 Feb, 2018 18:44
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?
Posted in: Frameshifts and IntronsCZ1 Tail assembly proteins
| posted 04 Feb, 2018 19:08
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?
Posted in: Functional AnnotationHead-tail connectors
| posted 03 Feb, 2018 17:05
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
Posted in: DNA MasterRunning DNA Master on a Mac using Wine
| posted 29 Jan, 2018 19:00
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
Posted in: AnnotationBest Gordonia model for GeneMark
| posted 12 Jan, 2018 17:50
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
Posted in: DNA MasterRunning DNA Master on a Mac using Wine
| posted 11 Jan, 2018 19:13
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. :-)
Posted in: DNA MasterRunning DNA Master on a Mac using Wine