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Recent Activity
All posts created by cdshaffer
Link to this post | posted 09 Nov, 2021 17:53 | |
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Wow thanks for this, you are correct that pham is missing. You have actually located a bug in Starterator, which crashes when you try to analyze that pham. This is excellent, as we find and fix these bugs the program works better and better. I did a quick check and I found the general location of the problematic pham in the analysis but will need time to dig deeper into why it is happening. I will post more info once I get this bug squashed. Thanks for posting. |
Posted in: Starterator → Pham not found in Starterator
Link to this post | posted 03 Nov, 2021 16:25 | |
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As usual we are in agreement. I too think it is a really strong candidate but I was just not going to call without something more in support. |
Posted in: Frameshifts and Introns → TAC frameshift in singleton
Link to this post | posted 01 Nov, 2021 19:58 | |
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OK, I have the situation in phage onionknight (a singleton) looking for a tail assembly chaperone and looking for the slip. The attached shows the region which is the only sequence that matches at all with any of the published slippery sequences. However, it is by no means an exact match. See pic, I have highlighted the putative slippery sequence in blue and the two translation frames in red. This would be a typical -1. This slip would be about 20 amino acids upstream of the stop codon in the short form so not an unreasonable location, it would just be nice to get a consensus with other annotators if this match to published slippery sequences is close enough to annotate or should we just leave it as two separate ORF's. |
Posted in: Frameshifts and Introns → TAC frameshift in singleton
Link to this post | posted 16 Sep, 2021 20:51 | |
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I will add my experience as another datapoint to help with troubleshooting: I too am also getting glimmer results but not GeneMark results, and I have confirmed the settings as displayed in Debbies attached picture. Very strange that one predictor would work and not the other for some users and not others. |
Posted in: DNA Master → Auto-annotation fix for fall 2017 and later
Link to this post | posted 13 Sep, 2021 18:04 | |
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That looks like a very low level issue with the disk device drivers. Very difficult to troubleshoot without a lot more details or direct access to your machine. I would try deleting this machine and rebuilding. You could also try the newer SEA 2020 VM. The good thing about that 2020 VM is it has the new pdm_utils installed. I don't know if I am allowed to post the link to the VM disk image in the open. Feel free to email and I can send you the link. |
Link to this post | posted 20 Aug, 2021 00:55 | |
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Nancy, These discrepancies typically happen due to the database updates coming out at different times for the different sites. things can often slow down a bit in the summer with vacations and the like as well. You can use these links if you want to see which version of the database is being used at each site: phagesdb see: http://databases.hatfull.org/Actino_Draft/Actino_Draft.version starterator see: http://phages.wustl.edu/starterator/database.version pecaan: look on any "pham maps" page just above the map phamerator.org: open the pull down menu in the top left Currently Starterator and Phamerator are behind on 424 and phagesdb is on 425, so you want to use the phamerator number to get to the starterator report. The instructions on the various ways to get to the starterator report if the one from phagesdb is not working can be found here: https://seaphagesbioinformatics.helpdocsonline.com/article-37 In this particular case, since you know you want pham 73206 you can just type the address out manually (or copy/paste this address ). http://phages.wustl.edu/starterator/Pham73206Report.pdf That page has the report on Ganymede_Draft gene 1. |
Posted in: Starterator → Pham not found in Starterator
Link to this post | posted 04 Aug, 2021 21:56 | |
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newer browsers have dropped support for the FTP: protocol. There was a while when firefox was working even though chrome was not, so try firefox. You can also try Dan's instructions here: https://seaphages.org/forums/post/8693/ Although if you read through the rest of that discussion, it appears lots of people are having trouble with new installs even though updates on already installed versions are still working. But I cannot tell if it is failing for everyone or just some new installs. Good luck. |
Posted in: DNA Master → Problem installing DNA Master on Windows 10
Link to this post | posted 04 Aug, 2021 21:46 | |
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It does not look like any of the cluster K1 phage in the sea phages database were found as prophages but the all of them are classified as temperate and the early phage for the cluster could make lysogens. See: Pope et al "Cluster K mycobacteriophages: insights into the evolutionary origins of mycobacteriophage TM4" |
Link to this post | posted 28 Jul, 2021 21:47 | |
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I just found this comment in the approved list in the notes for Cas4 family exonuclease which may be why some people may remember seeing hits to this Pfam before but never using it in a functional annotation:Cas4 family exonucleases - This family of exonucleases is similar to the exonuclease domain of RecB. The Cas4 label should be used if the gene includes only the exonuclease region. IF the gene also includes a helicase domain, the RecB label should be used. Cas4 family nucleases tend to have alignments to the crystal structure 3H4R_A and to the PD-(D/E)XK nuclease superfamily (PF12705.7, among others). I checked and there were a few HHPRED alignments between Cas4 and this Jada protein but they were very short (~25 aa) with scores of ~35%, so the "Cas4 family exonuclease" is not really appropriate for this small group of proteins. However, for many other proteins, with high quality alignments to both Cas4 and hits to PD-(D/E)XK, the Cas4 may be the better final annotation. Annotators should examine the lengths and qualities of the alignments to pick between all these various exonucleases. |
Link to this post | posted 26 Jul, 2021 23:40 | |
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I have run across a very clean HHPRED hit to the crystal structure 2OST in phage Jada (CDS 81782 - 82135) and Bartholomune (CDS 105264 - 105620). There are two more genes in the pham group, Braelyn_205 which is annotated NKF and Racecar_217 which is currently annotated "Holiday junction resolvase" and is quite a bit larger than the other three. For Jada the protein has an HHPRED hit with 99.9% probability and 99.1% coverage to the 2OST crystal. There are secondary hits to Holiday junction resolvases but these alignments are only about 45% coverage. This Jada protein also aligns in HHPRED to the Pfam PF11645 with 98.9% prob 98% coverage. the paper associated with this crystal is here: The restriction fold turns to the dark side: a bacterial homing endonuclease with a PD-(D/E)-XK motif. Yhis paper described a different type of endonuclease with a fold pattern and critical amino acids which is distinct from the more typical HNH endonucleases. Following the typical structure of our other endonucleases I would propose either "PD-(D/E)-XK endonuclease" based on the terms used in the above EMBO paper or the same without the dashes (i.e. PD(D/E)XK ) or the variant used with the Pfam "PD-(D/E)XK endonuclease" Note jada protein does not align to any of the other types of endonucleases (HNH, RusA, G-I-Y Y-I-G, or LAGLIDADG). |