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All posts created by lhughes

| posted 19 Nov, 2021 16:19
Awesome! Thanks, Debbie.

Lee
Posted in: tRNAsTomas tRNA error
| posted 19 Nov, 2021 14:52
I'm getting the following error back from the Phamerator import process for SEA_TOMAS_193 (Tomas_TRNA_40):

"ERROR: Evaluation ID: TRNA-EVAL-018. Status: error. Definition: Check if the tRNA coordinates appear to match the Aragorn or tRNAscan-SE prediction(s) for SEA_TOMAS_193 (Tomas_TRNA_40). The tRNA feature is expected to have coordinates that match Aragorn or tRNAscan-SE. Result: The tRNA coordinates (99205, 99279) appear to be incorrect. Left coordinate looks correct. Right coordinate should be moved left by 3 base(s). Status was changed from 'warning' to 'error' automatically due to no interactivity."

This tRNA does not show in the web-based Aragorn output. It has an infernal score of 38 in tRNA-Scan.

When I check the DNA Master file, the coordinates are different (99206-99279) so am confused by the message saying the left coordinate is correct (the message has a different number than my file) and that makes me question exactly what coordinate is meant by the suggestion to move the right coordinate to the left by 3. (In looking at this, I note that moving the coordinate left by one would leave a "CC" as the last two bases of the tRNA, which would seem to be in keeping with what would likely be expected based on the diagrams in the guide.)

I'm attaching a screenshot of the current call in the context of the genome sequence.

Suggestions on getting this right so it will import into Phamerator?

Lee
Posted in: tRNAsTomas tRNA error
| posted 18 Mar, 2021 03:09
Just to add from the perspective of a BE1 phage (looking at Cross, which we annotated last semester), the CCCGGAA that lines up with the CCCAAAT in the BK1 examples is preceded by a stop codon in the potential second reading frame (and looks to be that way in the majority of the BE1 examples in Chris's chart), so that is exactly the longest position where a frameshift could take place between those two reading frames in those phages. That's interesting (whether or not it really means anything).

Lee
Posted in: Frameshifts and IntronsNo frameshift in cluster BK1?
| posted 18 Mar, 2021 02:55
Looking at the referenced paper, I do find that the CCCAAAT appears very much like the GGGAAAT in the Lambda example. If we can follow that example, then the shift would be a -1 giving Proline (from a Proline in the original frame). The new frame had a stop codon a few codons previously, so this is about the earliest the frameshift could happen. This looks very good to me for the BK1 phages (though still begs the question about where a shift would be in the BE1 phage genes that are in the same pham).

The first nucleotide of the slippery sequence in Sham would be 23985 (this is the phage I had open to check).

Lee
Posted in: Frameshifts and IntronsNo frameshift in cluster BK1?
| posted 17 Mar, 2021 21:12
Joyce,

We've annotated several BK1 at UNT (and are annotating 2 right now). The last line of your post hits at the crux of the matter. Without a clear slippery sequence, we cannot bioinformatically identify a frameshift even if it seems likely that there could be a frameshift in this area. That is the reason none of the annotations I've been involved in for this subcluster have a frameshift in the final annotation.

Lee
Posted in: Frameshifts and IntronsNo frameshift in cluster BK1?
| posted 09 Mar, 2020 18:52
I *think* we've been trying to use "endolysin" unless it was specifically the Lysin A and B situation, so hopefully most of our more recent ones are already correct. Good to have the clarification.
Posted in: Cluster BD Annotation Tipslysin A
| posted 24 Feb, 2020 14:50
We see a similar region in the Cluster BI1 phages. When we look more closely at the Phamerator map, we also see the criss-crossing lines of short regions of homology that I see in the map of the Cluster DJ phages. There appear to be some short areas of conserved sequences between those genes (that is what we find in the BI1 phages). I would consider that these conserved sequences probably serve some purpose and are likely intergenic, so extending to LO just to do so might not be the best approach without further analysis of what is in those gaps. I have a graduate student who is doing that for BI1 phages right now to try to understand what is going on there better.
Lee
Posted in: Choosing Start SitesSD scoring matrix
| posted 02 Oct, 2019 19:05
welkin
Hi All,
Aragorn is back up and working.

Best,
Welkin

We are having trouble accessing Aragorn today. Anyone else having the same problem?

Lee
Posted in: tRNAsAragorn Issue
| posted 17 Aug, 2019 20:12
DrHHNZ
Thanks Claire,

That is helpful and we had seen some hints in the HHpred.
The students had suggested that the only matches were all "integrases" without any further designation. I will have to take a closer look when we are back in class again. Thanks again for your time!
Best,
Heather

Hi Heather - I think that is an NCBI issue. The hits used to say which they were, but I think more recently NCBI decided to use the generic "integrase" for everything so that information doesn't pop out like it used to.

Lee
Posted in: PECAANNew Features in PECAAN
| posted 26 May, 2019 19:47
Steven Caruso
These are big phages.

S.

Yep! At least the large terminal repeats actually bring the total down a little bit (since both ends should be identical, you only have to annotate one end and then just match the other one), but still large. And the massive number of tRNA's increases the workload too.

Lee
Posted in: tRNAsBE1 tRNAs