Link to this post | posted yesterday, 16:02

cdshaffer

Database 609 was released with 24 new phage. The whole starterator reports for these phage have been added to the collection found here: https://wustl.box.com/v/Actino-phage Pro Tip: Sort the file by date if you want to see the most recent files like the ones below: New phage in 609: BaconCheese Blesser Bogg DanSyl44 DeerParkTS Emmetator Fingolfin ForesterFrank FrumpyGal GaloreK Kelzog Lehmann LittleMinkey Mila11 Moby Moiqah Mwanjiwa OdetoJoy PeanutPie Prudy SlySloth Topiatin TpudiCK Triad

Link to this post | posted 11 Aug, 2025 16:01

cdshaffer

Database 608 was released with 24 new phage. The whole starterator reports for these phage have been added tot he collection found here: https://wustl.box.com/v/Actino-phage Pro Tip: Sort the file by date if you want to see the most recent files like the ones below: New phage in 608: Aloe25 Amoonguss Argena Balloona BillyBobJr Blackpen Bubble Bugg CaramelLatte ChickyNuggy Clammy CocoaPuff Davielle DeGene Dirtfootball ElJefes Gwennie Kavo Kimba Lynnae PestoPenguin RockieBear Wolpertinger Zilla

Link to this post | posted 29 Jul, 2025 17:24

cdshaffer

I did not do a deep dive into the critical side chains for these two activites. I just noted that the pham (currently 246509 ) had a dichotomy of annotations and both of these terms were used. An investigation into the nomenclature revealed that the terms were not synonyms nor are they different levels of specificity, there are, as you noted, quite distinct. So I used a few members of the pham in HHPRED searches and the results were consistent across the ones I tested. For PhluffyCoco_CDS_54, the HHPRED search were quite convinging: Of all PDB hits, there were 97 hits with probability scores above 90%. Of these there was only one crystal annotated with deaminase and about 20 crystals annotated with some variant of the transferase. Also of the top 10 hits (with probabilities ranging from 99.5 to 99.7 seven were annotated deoxyribosyltransferase. So the deaminase activity is simply not supported by the HHPRED results. Thus while the two proteins do share a common fold pattern (if I had to guess it would be a nucleotide binding domain) there is really little evidence for the annotation of deaminase and quite a good bit of evidence for the deoxyribosyltransferase. Edited 29 Jul, 2025 17:30

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