Link to this post | posted 23 Jul, 2025 05:33
cdshaffer	database 606 was released with 21 new phage. The whole starterator reports for these phage have been added to the collection found here: https://wustl.box.com/v/Actino-phage new phage in 606: Bellris Bubbykins Caitlin Celestialunch Cloudyecho CogOmlette Dirtdigger Elfy FiveHead Gachnar JohnThicc Nikan Origami PhuzzTulsa Rocha Spinach Sultana TraderJ WorldCup Xebius YasnayaPolyana

Link to this post | posted 23 Jul, 2025 05:30

cdshaffer

If you are writing an article and need to cite the tool phamerator: Cresawn SG, Bogel M, Day N, Jacobs-Sera D, Hendrix RW, Hatfull GF. 2011. Phamerator: a bioinformatic tool for comparative bacteriophage genomics. BMC Bioinformatics 12:395. Phamerator can use many different databases. If you go to the front page of phamerator on the web, the database you are using is selected at the top left. Since you are asking here I will assume you are using the main Actino_Draft database. However other specialized databases are availabe to some users, this is why you must login to use phamerator. If you want the current version of the Actino_Draft database it is always posted here: https://databases.hatfull.org/Actino_Draft/. On that page if you click on the Actino_Draft.version link you will see the current version which as of yesterday July 21st 2025 was v606. PECAAN, Phamerator and Phagesdb all update automatically as each version is released. This can be confirmed in various ways depending on the web site.

Link to this post | posted 14 Jul, 2025 21:51

cdshaffer

There is a region in many AS phage (typically around 18 - 23 kb) where genemark and glimmer call different genes on different strands. These genes often have very large or complete overlap. This is unusual in the extreme and finding the proper strand is a known weakness of these ab initio gene finders. As such be very suspicious of genes which overlap and are on two different strands. To call both you need very strong evidence, ideally mass spec results showing translation of both frames. However extremely high quality HHPRED hits for both potential predicted protein products might also suffice. Without extremely strong support, review the evidence and pick one gene and delete the other following the rules as outlined in the annotation guides. Edited 14 Jul, 2025 21:53

Link to this post | posted 12 Jul, 2025 21:11
cdshaffer	database 605 was released with 3 new phage. The whole starterator reports for these phage have been added to the collection found here: https://wustl.box.com/v/Actino-phage new phage in 603: Bezza LookingGlass OrediggerDelux

Link to this post | posted 02 Jul, 2025 04:06
cdshaffer	database 603 was released with 4 new phage. The whole starterator reports for these phage have been added to the collection found here: https://wustl.box.com/v/Actino-phage new phage in 603: Wolfwood Pisa4 Demure Colossa

Link to this post | posted 19 Jun, 2025 20:29
cdshaffer	As of 2020 there is a new rule, you should have a lysin B if you are annotating a lysin A. If you cannot find a lysin B just annotate endolysin. See this discussion: https://seaphages.org/forums/topic/4656/

Link to this post | posted 18 Jun, 2025 21:18

cdshaffer

There is a protein in this cluster which has been annotated with two different functions: deoxycytidylate deaminase and nucleoside deoxyribosyltransferase. Check the pham for this protein: PhluffyCoco_CDS_54. These two enzymes appear to be related and have an ancient common ancestor but these two enzyme activities are quite different. Be wary of BLAST alignments for this function and focus on the top HHPRED alignments or 3D predictions. For several phages in the AS cluster the HHPRED evidence is clear these are nucleoside deoxyribosyltransferase. Edited 24 Jul, 2025 17:33

Link to this post | posted 17 Jun, 2025 15:41
cdshaffer	for more discussion on this matter see this discussion: https://seaphages.org/forums/topic/5775/

Link to this post | posted 14 Jun, 2025 01:53
cdshaffer	Database 602 was released with 15 new phage. The whole starterator reports for these phage have been added to collection found here: https://wustl.box.com/v/Actino-phage New Phage released in 602: Chaewon DaRealMyers Ding FremontTroll Labradorite Mikronejon Montavir Peridot RegnumDei Sangak SassyC SuperSonics Trice Virizion Zarafa Edited 02 Jul, 2025 04:07

Link to this post | posted 03 Jun, 2025 17:18

cdshaffer

We had a recent putative RecA that had some curious results so am following up on the "How to call a RecA". Our protein had what appeared to be two significant differences to the standard model. One of the hydrolytic residues did not appear to be present and the C-terminal Mg binding domain was totally missing. See the attached for more details but the final result was that our protein was still a RecA once we investigated, and shows the limits of HHPRED and the idea that anything conserved is necessary for activity. 953Kb