Link to this post | posted 29 Mar, 2025 02:09
cdshaffer	Database 593 was released with 5 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 593: FatCactus, Liberone, Neuvillette, RoseMarie, and Rossetti

Link to this post | posted 22 Mar, 2025 00:56
cdshaffer	Database 592 was released with one new phage. The whole starterator report for this phage has been added to collection here: https://wustl.box.com/v/Actino-phage Phage Released in 592: WileyE

Link to this post | posted 14 Mar, 2025 16:56

cdshaffer

Here is a simple example with super simple sequences: query = AAA subject = CCCAAATTTGGG When blast does the alignment with appropriate settings (since blast would never show this by default as it is too short, but you can force it) and you would in theory get this result: 1 AAA 3 ||| 4 AAA 6 The %aligned is 100% because the entire query is found in the alignment the % coverage is 25% since only 3 bases of the 12 bases in the subject are in the alignment For % identity you get 100 % because 100% of the bases in the alignment match identically For DNA there is no %similar (the % similar is only used for amino acids alignment) but for a.a you just would count the fraction of alignment columns that are either identical or similar and divide by the length of the alignment. CCD is a database of protein domains (i.e. small parts of proteins seen widely) think things like zinc finger or ATP binding domain. Thus, for interpretation of CCD hits hits you care most about the % coverage and % similar the % aligned is mostly irrelevant.

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