Link to this post | posted 22 May, 2018 00:07
cdshaffer	That message is a warning not an error. It comes up because it is easy to get duplicate genes if you use the DNA Master tool to merge multiple DNA Master files. In this case however, you have two genes, a short form and a long form of the TAC with the same 5' end and this is exactly what you want. So it is OK to ignore the warning.

Link to this post | posted 15 May, 2018 14:21

cdshaffer

OK, I did a quick google search on that error. It appears to be a WINE error code not a DNA Master error code. So, I tried a search using DNA Master on my mac with WINE and I too got that same OLE 80040152 error. I suggest you repost your question in the Running DNA Master on a Mac using Wine thread there are a few people who post there regularly with lots of WINE experience that might have seen and solved this issue. Edited 15 May, 2018 14:39

Link to this post | posted 14 May, 2018 19:03
cdshaffer	just tried on my Win7 machine with the April 2018 update and a single BLAST search, that worked and was able to get results. Since it is peak hours I did not try a BLAST all. Edited 14 May, 2018 20:11

Link to this post | posted 10 May, 2018 21:40

cdshaffer

I just help a student yesterday install the WINE version on yer mac and after we installed, ran the updater and restarted DNA Master things just didn't look right. So I had the student check in the Help -> about menu. Sure enough, the auto-update had failed even though I saw her run the update and there were no error messages. We re-ran the auto-update again and it worked the second time. So I would recommend you double check to make sure the installed version is the one from April 2018.

Link to this post | posted 06 May, 2018 20:55
cdshaffer	The updated phamerator database has now been fully run though starterator and the results have been posted. You will now find your report available: http://phages.wustl.edu/starterator/Pham45669Report.pdf Edited 07 May, 2018 03:12

Link to this post | posted 26 Apr, 2018 20:33

cdshaffer

Just a note in case someone comes to this thread later, in cases where the pack/unpack protocol doesn't work. Before you start over from scratch to redo all your annotations in a new DNA Master file you can try to at least transfer the notes and annotations using the technique Welkin describes in this post: https://seaphages.org/forums/topic/4547/?page=1#post-6264 That technique has saved me many times.

Link to this post | posted 26 Apr, 2018 16:00

cdshaffer

An HHpred search shows weak evidence for a terminase with matches of 95% (e .11) to COG3747; Phage terminase, small subunit, and to PF05119 Terminase_4 Phage terminase, small subunit 94% (e .24). The issue here is you won't find those if you use the default PDB database, you have to add the other databases before you do the search. See this page for the list of databases: https://seaphagesbioinformatics.helpdocsonline.com/article-19 I would say the evidence is pretty weak on its own but if you look at this page: https://seaphagesbioinformatics.helpdocsonline.com/article-91 you will see that at least one but no more than two terminase proteins must be present somewhere in your phage's genome. So annotation of this gene probably depends on if you have better evidence that some other gene or genes have stronger support for being a terminase, in which case one would probably argue that this protein is, as you suggest, a distant relative of a terminase but is not THE terminase. On the other hand if no other protein in the genome has even a hint of being a terminase then I think that combining the expectation that there must be a terminase somewhere with the hhpred hits is strong enough to justify the terminase annotation.

Link to this post | posted 20 Apr, 2018 16:59
cdshaffer	Working link: http://www.techrepublic.com/blog/windows-and-office/selectively-disable-uac-for-your-trusted-vista-applications/

Link to this post | posted 19 Apr, 2018 05:32

cdshaffer

I must say I really like this gene cluster. I use it as a great didactic opportunity to have students think carefully about biochemistry and the nature of enzymes. I remind them that all an enzyme can do is speed up the reaction rate, it cannot control "the direction" of the reaction. The direction depends on which substrates are in excess. This is especially an issue when enzymes are purified and studied in vitro where substrate concentrations can be orders of magnitude different than intracellular levels. This leads to confusion when trying to functionally annotate and this cluster is a great example. The top hit from hhpred is called an RNA Ligase on the short text but when you dig into the enzyme it all makes sense. The pdb entry for this RNA Ligase is 1IUH. Here is the link: https://www.rcsb.org/structure/1iUH If you go to the page and click on the "annotations" tab you will see down in the "molecular function" section that this one enzyme lists both an RNA ligase and a 2' 3' Cyclic Nucleotide 3' Phosphodiesterase activity are listed. This is because experimenters can detect both activities in vitro. Some labs put in the cyclic nucleotide and see breakage of the phosphate to carbon bond (phosphodiesterase). A different set of substrates and you can drive the reaction the other way and create a phosphate to carbon bond (ligase). As for annotation, of the available approved terms, I feel like RNA ligase is the best available term since phosphodiesterase is not available. Phosphoesterase just feels too generic since there are many phosphoesterases that are not phosphodiesterases.

Link to this post | posted 23 Feb, 2018 20:24

cdshaffer

It is not unusual to get slightly different results from gene predictors when the same sequence is analyzed on different computers. Software version, default parameter settings, different training sets and other factors can effect the outcome. This is really just par for the course in bioinformatics. Without good evidence to the contrary I always treat each source (PECAAN, DNAMaster, Phamerator) as evidence to be used in the final annotation. Those genes that appear in one auto-annotation and not the other simply have less evidence to support them being in the final annotation. From the Guiding Principles of Bacteriophage Genome Annotation rule 2 we know that genes rarely overlap by more than 30 bp, so clearly some of those genes in that cluster as displayed in the phamerator map should not end up in the final annotation. So the genes in that region that show up in both have slightly more evidence supporting their existence compared to the genes that only show up in one. However, you will want to use all sources of evidence before you decide which genes should end up in your final annotation. See Deciding whether an auto-annotated gene is a gene.