Link to this post | posted 22 Jan, 2026 19:20

cdshaffer

The RBS score is in PECAAN, it is called "final score" in the the table at the top that lists all the start codons. That table also has the gap score. This works OK for looking for large gaps that might indicate a missing gene. There is also a graphical map in PECAAN in the "Pham maps" tab. It is not as nice as the frames view (especially for student understanding of frames). It also does not have a way to zoom in/out so if you need specific details on a region it takes more work than using the frames map where it is easy to zoom in. Instead I typically just hover my moues over each gene to get the exact coordinates and then use mental math to get an idea of the exact gap/overlap. There is also a view something like DNA master's 6 frame view with the DNA and all the amino aicds, that is in the Sequence tab, but you have to scroll down to see it.

Link to this post | posted 21 Jan, 2026 17:01
cdshaffer	phage Overpar is posted. It was a new phage in release 629 so it was automatically processed a couple weeks ago. Enjoy!

Link to this post | posted 18 Jan, 2026 19:12

cdshaffer

Database 630 was released with 47 new phage. The whole phage starterator reports for these phage and for 1 request have been added to the collection found here: https://wustl.box.com/v/Actino-phage New phage since the last update: Aldrich Altjira Aonishiki Ayanochan BennyP BlacksBerry Blanky BloominB BronnyJr Budgie CheeseSpider ChristmasHams Crescenzo Cubone DarwinJr Florence1 Florence4 Forester FruityLoops Gerri43 Happabalu HogWash Jeilious Kureo Lavahound MilleFeuille Mulaychimus MurphyJoseph NonchalantPear Nyilah Pisa1 Popstraw Pupusa Rira Roberts ShadowBud Shroomer SirBeanington Solimine Spain SteakFry Stillion SuperHands Thales Tonaltzin YangYin YoyoKar Other phage processed: Bavilard

Link to this post | posted 16 Jan, 2026 22:18

cdshaffer

Starting in 2026, I have updated the code so that the results in the "_struct.txt" file can be directly loaded directly into the https://rnacentral.org/r2dt web page. So just to re-iterate all of the above: Current SEA-PHAGES annotation policy is that you do not need to run tRNAScan-SE for annotation; but if you want to, you can, just be sure to note this in your submission files so the QC team knows to also include tRNAScan in the QC protocol. If the tRNAScan web page is down you can go here to retrieve the tRNAScan analysis of your phage: http://phages.wustl.edu/trnascan/ and download a zip archive of the tRNAScan analysis of your phage genome. Edited 20 Jan, 2026 17:19

Link to this post | posted 16 Jan, 2026 17:35
cdshaffer	Yes I will add it to the list and process it with the next database release, which should be today but could be over the weekend.

Link to this post | posted 12 Jan, 2026 22:49

cdshaffer

Database 629 was released with 130 new phage. The whole phage starterator report for these phage have been added to the collection found here: https://wustl.box.com/v/Actino-phage As a reminder use sort by date to bring the most recent reports to the top of the list. New phage since the last update: AcciDwight Agamotto AirForce1 Aleia Amanises Amphitrite Anandi Artu Azaz BananenDer11 Barbonzobean BasketStar BellaJr BetaFish BigAnti BobaPhatt Boise BooTeria Bouclier Bowman Brewer Brizzy CardboardBox CartmannCramer Casab Cassini ChamoyPickle Charminar Chicken ChipsNGuac CosmicBrownie DeluluLabubu Demikore Dessert Ditters Divya DreamEater ERHickory Espio Farrylious FelixTres FirePit Fixie Flake Flutur FountainFog Gallop Glintora GodSpeed GoneGirl Gooberta GrimEater GumGum Hereford Hidrated Imara JeanClaude JeNeSaisPas Jeremy4pt0 JoyceMaria Kamdara KekoraPapaka Klodlith Kouch Laphuphu24k Larson LastNadiia LeBruni LilJank LilSaint LittleDigger Lucia Makima Mapleville Marichuy Mariel Maupel MegTheThird Merpity MillySue Minispark Mireles Monse Music NewKitty Niblet Orkz OverPar PallasAthena Pauu Pemberton PharkleMinkus Phloodle PoeMe PondAmelia PorkBelly Puppet Rattrick Ravana RedRaider89 Ren19 Renkei Rootkit7 Ruriko Sachet SallyH Salvatore2000 Shen Shynx SoilSleuth Sorvannah Spartan Stardrop Stellammi SteMason SunnyJune SuperheroCarly Tailonex Tairn4Wing TeamEdward ThursdayNight ToastyOats Toodles TripleC Tuti Vortrix Wigberry Winchester007 YoshiYama Zixiang Edited 12 Jan, 2026 22:51

Link to this post | posted 18 Dec, 2025 19:07

cdshaffer

We have now updated the Starterator servers to support the https: protocol so users should no longer get the "Not found" error due to this particular reason. Also as a reminder, you may want to download the whole phage report. See this thread in the forum: https://seaphages.org/forums/topic/5752/ for details. Or just go here to find all the folders with the reports for all phage posted in 2025: https://wustl.box.com/v/Actino-phage Edited 20 Dec, 2025 18:40

Link to this post | posted 07 Dec, 2025 16:44
cdshaffer	Database 627 was released with 11 new phage. The whole phage starterator report for these phage have been added to the collection found here: https://wustl.box.com/v/Actino-phage New phage since the last update: BoogieWoogie CatBus DartGoblin DingDing DoubleChamp FleetyMac GroundGoblin HomeFry KikiBouba Noxious PowerRanger

Link to this post | posted 05 Dec, 2025 21:56

cdshaffer

Wow this is great work. Really good analysis on using alpha fold to discover the very likely localization and biological role for these proteins. I would say this goes way beyond what is expected for a typical annotation but really good work. Love the correlation of alphafold size predictions and physical observation in the EM. I only have one comment that really that has nothing to do with the role and function of these proteins but has more to do with nomenclature and a not that uncommon problem, so I think it is worth bringing up. If you look at the approved terms list you will see that Dit is mentioned twice. One approved term is just Dit and the other approved term is Dit/tail tip cage. Why is there two different terms and how would one know which one to pick? All this comes from the cryo EM work of Bxb1 done by Krista in the Hatfull lab. When she looked at gp32 in Bxb1 it is sitting right here where your protein is and she said that this Bxb1 protein is a fusion of two previously described proteins Dit and tail tip cage. Dit is the N terminal part of this Bxb1 protein and tail tip cage is the C term. So she named this with that double label. So I am seeing lots of good work that this protein is a Dit but I wonder, is it like Bxb1 and is it a fusion or is your phage the kind where the Dit and the tail tip cage are two separate polypeptides? I did not do an exhaustive search (sorry too much grading to do before grades are due), I did take Baconcheese 40 and do an HHPRED search to PDB, there was a very nice hit to the actual structure of that Bxb1 Dit/tail tip cage (9D93_Mf). Interestingly the alignment is not full length, only aa 75 to 275 of the 450 aa long BaconCheese protein aligned to aa 30 - 236 of the 685 aa Bxb1 Dit/tail tip cage. So the only part that is matching is the N term which is the Dit part. So my preliminary results would further support your annotation of just "Dit". If you want to dig deeper still, I would investigate what those unaligned amino acids at the C-term might be? They don't align to Bxb1 Dit/tail tip cage but they could align to some other tail tip cage or to something entirely different. Bottom line: I would certainly put my name on a paper that annotated this BaconCheese protein as Dit, but there might be something else going on here worthy of annotation at that C terminal end and a bit of further work might find it. On the other hand, an annotator always has to, at some point, say: "enough is enough, time to make the call" since there is not infinite time to investigate every protein. And so calling the "enough is enough" and annotating it Dit is totally fine in my book.

Link to this post | posted 29 Nov, 2025 02:44
cdshaffer	So sorry I missed this message. I usually come to this thread every week but we have had no new phage since middle of October. I have posted phage Phrampa in the O..R folder here: https://wustl.box.com/v/Actino-phage