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Recent Activity
All posts created by debbie
| Link to this post | posted 13 Feb, 2023 13:45 | |
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Amanda, This answer is all about context. I don't know the answer with the information provided. Look at the whole genome. What makes sense? Now that we know that N terminal hits can be signal proteins, i think where in the gene the membrane protein is found impacts my thinking. Just because we moved to Deep THHMM doesn't mean you can't use other tools to continue your evaluation. In general, keep it simple. Membrane proteins are not functions. And when Phamerator gets this in place, the data is not lost. debbie |
Posted in: Annotation → Membrane proteins
| Link to this post | posted 12 Feb, 2023 23:19 | |
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Rick, For now, I would call the big overlap, which I assume is the way that Survivors was called. Let's continue to consider the Guiding Principles as guidelines. debbie |
Posted in: Cluster CT Annotations Tips → BIG GENE OVERLAP
| Link to this post | posted 08 Feb, 2023 03:15 | |
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Amanda, I vote for not calling any TACs. debbie |
Posted in: Cluster B Annotation Tips → Tail assembly chaperones?
| Link to this post | posted 03 Feb, 2023 20:19 | |
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From HHPred, this gene hits HK97_gp10, a minor capsid protein and a tail protein. So one must ask which is it? HK97 is the prototype phage for understanding how the capsid is formed. The lab that studied it was the lab of Roger Hendrix, from the University of Pittsburgh. As we hit gp10 of HK97, I asked if they knew the function of that gene and they could not identify it in their studies. As per the Approved Function List, when you hit HK97_gp10, stick with Hypothetical Protein until someone finds more data to support a call. |
Posted in: Cluster EJ Annotation Tips → Potential minor capsid protein
| Link to this post | posted 02 Feb, 2023 00:09 | |
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My advice is to ask the IT administrator to set the preferences. Whatever they do, should stick. debbie |
Posted in: DNA Master → DNA Master errors
| Link to this post | posted 29 Jan, 2023 21:50 | |
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Hi Robert, Please check you DNA master preferences and make sure you follow #2 and #6 correctly. https://seaphagesbioinformatics.helpdocsonline.com/article-66 |
Posted in: DNA Master → Glimmer failure during autoannotation
| Link to this post | posted 26 Jan, 2023 23:45 | |
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Nope, not yet. all help is welcome! debbie |
| Link to this post | posted 20 Jan, 2023 15:37 | |
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Holly, Exactly! You've got it! debbie |
Posted in: Functional Annotation → Scaffolding protein
| Link to this post | posted 20 Jan, 2023 03:24 | |
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Hi Holly, hmmm. I think that Mopey_14 (stop codon 10436), can be called the scaffolding protein because of the InterPro hit at HHPred (Q38580). It is a 99.5% probability (evalue is e-12) and has protein homology to the scaffolding protein of SPP1 (evidence is from UniProt database. Granted that the example used by the approved function list is D29, but your protein doesn't have to hit the example (and it doesn't, does it?) |
Posted in: Functional Annotation → Scaffolding protein
| Link to this post | posted 17 Jan, 2023 14:11 | |
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Hi Amy, There are lots of reasons why Glimmer and GeneMark don't call the same things exactly the same. Mostly their algorithms are different. and the math breaks down with small proteins. It is why we use both. And they can both miss a call and predict something that we throw away. If automation made the best calls, we would not be doing this one gene at a time. debbie |