Link to this post | posted 10 Mar, 2025 19:30

cdshaffer

I always remind my students of rule 9 in cases like this as a good first bit of evidence: 9. Switches in gene orientation (from forward to reverse, or vice versa) are relatively rare. In other words, it is common to find groups of genes transcribed in the same direction. so if all the neighbor genes are on one strand then of the two predictions, I generally prefer the one on the same strand (there are rare cases of a single gene on the opposite strand, so use the Pollenz method described above to check for that). Another thing I have students do is run both predicted protein sequences through HHPRED. I think a true gene is much more likely to have an HHPRED hit as compared to a false positive ORF on the other strand. You don't need to see >90% probability, if one gene has HHPRED hits in the 70-80% probability and the other gene has a hits in the <40% probability, you have found good evidence which is likely the true gene and which is the false positive.

Link to this post | posted 16 Feb, 2025 15:37

cdshaffer

Database 587 has been released and the following whole phage reports have been added to the collection. See the first message in this thread for more info, these folders contain all the reports: https://wustl.box.com/v/Actino-phage Phage released in 587: BarrowTuph, Becksu, Bhagsy, Bigchungi, Bigflo, Bobquesha, Brookers, Corium, DeejaClivia, Doughnut, EmiMonkey, Emmaloid, EnzoK, Etoile, FoghornLeghorn, Gratitude, KingJulian, Lebo14, Levia, LionsBait, Lowa, LunarLander, Marco3, Nekros, Nette, NewHope4, Olivio, Phalaborwa, PhineBark, PhlipPhlop, Phlippers, Plata, Polo2Bam, Prinashe11, Razzleberry, Rearden, Riverton, Sabourin, Shaboozey, SilverChicken, Slim, Stuck, Stuu, Teejan, Terrific, TooFast2Furius, Violac

Link to this post | posted 10 Feb, 2025 15:21
cdshaffer	Database 586 has been released and the following whole phage reports have been added to the collection. See the first message in this thread for more info, these folders contain all the reports: https://wustl.box.com/v/Actino-phage Phage released in 585: Faiyaz, Giorgio, Gumpizza, Lea83, Mayonnaise, Polyphemus, RockScotty, Spiderbri, Tortoise12, Tristan

Link to this post | posted 07 Feb, 2025 18:25
cdshaffer	Just adding a note here in case anyone searches and finds this thread later. The powerpoint and video on the topic of RecA & ATPases are discussed here in this thread.

Link to this post | posted 06 Feb, 2025 06:18

cdshaffer

Database 585 has been released and the following whole phage reports have been added to the collection. See the original message in this thread for more info and this folder to download your report: https://wustl.box.com/v/Actino-phage also be aware that the current code for determining if a phage is "new" and should be run is a bit wonky and I am not sure it is working correctly, so if you have a new phage and it is not in the proper folder in the above link send me an email so I can track down the issue. This is the only way to get better code so please send inquiries if you cannot find your phage. Phage Released in 585: AksarBAT, Anilorac, ApoKipo, Applecrisp, Bramble, Casablancas, Causa, Cheesepuff, Chipette, Cygnet, HairyMan, Jant, Jella, KingPhillip3, KleverKiS, Kosier, LavAbarElk, Marleymoo, McSinger, MicyPS, OtsoOtso, P3MA, PSirce, RosieMae, Schism, Shenandoah, SirBeauregard, StormChicken, Subaru, Sweetclover, Tchotchke, Thimble, Tongui

Link to this post | posted 27 Jan, 2025 17:44

cdshaffer

I don't know how much control you have with the PC and the white board, but if you have access to the video setting you can try to lower the resolution of the screen on the PC and see how the white board responds. DNA master is using a static font, so the letters are always a certain number of pixels. If you can change the screen resolution (in the most ridiculous case change it to 800X1200) then each pixel becomes larger and the DNA master window should become larger. However, if you are using a PC in a classroom the PC is probably locked down, worth a try but no guarantee.

Link to this post | posted 25 Jan, 2025 17:52

cdshaffer

Database 584 has been released and the following whole phage reports have been added to the collection. See the original message in this thread for more info and this folder to download your report: https://wustl.box.com/v/Actino-phage Phage in release 584: Babushka, Chavito, CheeseDanish, DanHam62, Donatella, Egi03, Fongie, GoodLuckBabe, Guinevere, HeadMave, HerbBucket, Iqorha, JellyBread, JimmyPG, LadyJasley, Marlia, Mentos, Milomuff, MUWow, Panchaali, Parvaparticeps, Penoan, Pize, Primadonna, PrinceCharming, Red305, Socotra, SoJulia, Solea, Stormer, Trufflozitus, TwoBits, Violeta, Wogge42 Edited 06 Feb, 2025 06:18

Link to this post | posted 22 Jan, 2025 22:38

cdshaffer

TL;DR: improvements to the back-end now allow for whole phage starterator reports to be generated for all new phage. See phage list at bottom to see if your phage is in release 583. Reports can be found at https://wustl.box.com/v/Actino-phage I have had some time to update the infrastructure and get Starterator to run inside a Docker container. This has allowed me to move the processing to the WashU cluster with significantly more processing power. I have added code to now run "Whole phage" reports in bulk on every new phage. As an initial release I am posting the whole phage reports for all phage which have been added since early Dec 2024. The whole phage reports, focus the starterator results on a single phage and have three benefits. First, the reports will sort the image section so that track #1 will be the gene for your phage. Thus, users will not have to sort through the tracks to find their gene. Secondly, the summary notes have been shortened to only your phage making this section shorter and easier to read. Finally there is a table generated near the start of the report which examines the current annotated start and compares it to the other manually annotated starts from that pham and summarizes that comparison. This allows for very rapid identification of starts that agree with the consensus found within the pham and those which do not. The downside is that for large phage from large clusters the whole phage report itself can be large and cumbersome so depending on your phage it may still work better for you and your students to use the individual pham reports. I have generated reports for all phage added since early December. See the complete list below. Here is the folder: https://wustl.box.com/v/Actino-phage P.S. If you have an older phage and would like a whole phage starterator report let me know by email and I will add it to the next run. Also all questions/comments/suggestions should be sent to me. Chris Shaffer Here is the list of phage found is this collection: Ablatia, Acai, AdaS, Akino08, Alatato, Amo99, AngelCake, Artiphact, Astralis, Axiom, BabyMoney, BaronJohn, Beleetus, Belieber, BetterYeti, BigDome, Bimmel, BlessJoy, BlueShadow, Bouchard, CallaLilly, CarisSwetlik, Carrillo, Caspiboi, ChickenTender, Chilliams, Chlochlo, ChocoMunchkin, Circuit, Citrus, CookieDog, CupcakePrincess, Dancer, Demure, Destructrice, DillyDally, DirtPie, Dodo, DogYard, EGUnicorn, ELee24, ElectricPheel, EmoNemo, ForDig, Forrestell, FosterFrank, FreakyGoo, FuegoCuervo, GUPitcher, Gandionco, Garnacho, Gavriela, Glorp, Glotell, GoldDust, GoldenEssence, Goodgraces, GoongGoong, Gravel, Greenbelt, Guzman, Gwennie1, Halloweekend, HamCheese, HazuAndZazu, HollowPurple, HotPotato, Ichiang, Invectra, Iridessa, IsHungry, Issa7, Jabb, Jakelyne, Jankie, Jesabah, JessellCookie, Jezreel, Jingles, KNG13, KSunshine22, KendraB23, KevinMinion, Khan1, Kinny, Koan, Kolhan, Kropertea, Kubulix, LadyAstra, LeoJr, Lethe, LilSmirk, Linayshia, Lishka, LordBart, Losacky, LucySwiss, Lukepolites, MacKat, MajinBuu, MakCheese, Marsus, Maruru, MaterMagnus, Mesmerelda, MiamiPanther, Moonflower, MsUbiquitous, Myram, Natasha, Nathan, Navi1117, NoSwimming, Nostromo, Nova53, November, Ollypop, Olympi, Pelletreau, Phanita, PhedwardCullen, PhigPhack, PhillyJawn, Phroglets, Pochacco, Poochiewood, Powelldog, PrairieDogTown, Raid, Rattail, RazorC, RazzB, RedRaider, RenegadeRaider, Rikishi, Riptide, Rita130, Rockabye, RustyBoy, SVoro, Scissor2024, Scotia, Scuba, Seldom, SenorClean, Shaffner, ShawBrad, Shrubaron, Shuckle, ShyRosie, SilentWarrior, SirFrank, Skitty, Smelly, Softsoap, Spooks, Starburst, StuartMinion, Sunshine23, SwainyDoc, SwissCheezer, Symere, Talon44, Talos, TicTac, TinaBug, TinyTerror, Toad24, Toneprano, Towmatter, TownLake, Trackstar, TriFive, Tubberson, Underpass, Utopia, Vitaenoii, Vitus, Vivum, WaddleDee, Wardwill, Westrich, Westy, Windest, Worcestershire, Wrackline, Yeshua, Zahlia, Zebo, Zhuangyuan, Zippen, Zodiariah, Edited 22 Jan, 2025 22:40

Link to this post | posted 09 Jul, 2024 21:25

cdshaffer

The RecA like proteins in the BN cluster are not placed in the same pham and the highly likely RecA (exemplified by Spud_205). See this discussion for details: See this forum post #5567. As such care should be taken when annotating a protein as a RecA and the less specific term "ASCE ATPase" should be used unless there is clear evidence for the presence of all the important features to support the RecA annotation (again see topic 5567 linked above)

Link to this post | posted 29 Jun, 2024 18:59

cdshaffer

Recent crystal's have supported the annotation of both a large and small subunit. See the Crystal 7JOQ. If you have sufficiently good matches to this crystal it can support the indentification of the small terminase in BE phage. If you have a small terminase be sure to call the other terminase the large terminase. If you only can find support for one, just annotate simply terminase. Edited 03 Jul, 2024 17:03