Link to this post | posted 13 Sep, 2021 18:04

cdshaffer

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. Edited 13 Sep, 2021 18:04

Link to this post | posted 20 Aug, 2021 00:55

cdshaffer

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.

Link to this post | posted 04 Aug, 2021 21:56

cdshaffer

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. Edited 04 Aug, 2021 22:11

Link to this post | posted 04 Aug, 2021 21:46
cdshaffer	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

cdshaffer

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

cdshaffer

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). Edited 26 Jul, 2021 23:50

Link to this post | posted 21 Jul, 2021 17:28

cdshaffer

I have seen this behavior before but for me it is almost always if I submit a sequence for a phage that is not yet in the phamerator database. So it never surprised me there were no links as there was noghing in the phamerator database to link to yet. The work around is to use the pham links in the phagesdb blast results. Those links in the right hand column link to the phagesdb page for the pham report which have links to the starterator page. One think you might also want to try (which I have had variable success) is to go to the admin page, search for your phage name in the Phage table and click the edit button. Then see what phage it matching in the "Phamerator Phage Match" menu. For phage that I have that are not in the phamerator database I try to pick the phage most similar to my phage by BLAST, but you might also want to see if your phage is on the list and is selected. You might have to be the "owner" of the phage for that to work. Not sure.

Link to this post | posted 07 Jul, 2021 18:18
cdshaffer	Claire and (presumably) Dex and any other coders, thanks for fixing this bug and all the work you do to keep updating and improving PECAAN.

Link to this post | posted 21 Jun, 2021 22:01

cdshaffer

Thanks for being patient, I have been away visiting my sister There have been some issues with phagesdb pham assignments lately. So phamerator.org, Starterator and PECAAN all agree with each other but phagesdb has those same genes in a different pham, thus the link from phagesdb to starterator will not work. I just checked a few genes in Tarkin and could not find any broken links, so the most recent update to version 414 may have fixed things. If not, the best thing to do is double check the pham number on phamerator.org that should give you the correct pham number for the starterator report. I do appreciate the desire to delay some curriculum until students are somewhat comfortable with the the basics, I do the same with my class. So if you have not introduced phamerator.org or PECAAN you can use the "whole phage" starterator report. When I use these reports I just use the search feature in my PDF viewer to search for the stop coordinate, this will usually only appear in the top table and the last page of the report for the gene. I then scroll up to find all the other bits. The "whole phage" Starterator report for phage Tarkin is available here: https://wustl.box.com/s/7xsd2c9zvh44iob96avgdqa3urh3uwzy P.S. For anyone else, feel free to post a request here for a whole phage report or send a request by email. They take about 3 minutes of my time to start the process and about 2 minutes to post once the analysis is done, so happy to post reports for any requests.

Link to this post | posted 09 Jun, 2021 18:06
cdshaffer	As a follow up, Here is a PDF I created with examples from Starterator and how to interpret them. It goes from simple/obvious interpretation to more subtle. Unfortunately it is not an exhaustive set of examples but I think it did help my students. Starterator_examples.pdf Edited 18 Jan, 2022 04:33