Link to this post | posted 07 Jun, 2023 20:23

debbie

Lee, The confusing part of Kathleen's post is the sentence that states "But we don't understand why Starterator didn't call the most annotated start." But she is here today so we are able to discuss. The reason that Starterator doesn't make the right call is becuase it only reports what is in in the files submitted to phamerator. –Meaning in this particular case, Frankenweenie's auto-annotated is not what others ID'd as the best start to call. In fact, Kathleen and her students went to Starterator to justify making a change. That sentence in Starterator is to be coupled with the yellow line in the Frankenweenie graph and recogonized as in DRAFT form. What Kathleen and her students wanted was for Starterator to make the right call. Technically, it makes NO calls and just reports what was called (making human calls green and auto calls yellow).

Link to this post | posted 06 Jun, 2023 02:55

debbie

Hi all, There are (were) 2 strains of Arthrobacter globiformis from NRRL at Pitt that got distributed as A. globiformis NRRL B- 2979 SEA. They are A. globiformis NRRL B- 2979 SEA and A. globiformis NRRL B-2880 SEA. It is believed that one of the errors occurred in Spring shipments of 2019. However, we can't be sure, so we are asking that all A. globi strains be tested. Both strains have been sequenced and primers are designed to detect each strain. Protocol is attached here. First step is that if you have A. globiformis at your institution, please verify which one you have using the attached protocol. Second step, check phagesDB that all phages found on that strain are entered correctly. If not please make changes. If the number of phage hosts to be changed is small, use "Modify Phage" to correct. If you have many phage hosts to correct, you can send Dan (dar78@pitt.edu) a message to get the entries changed in bulk. Please send an email to inof@seaphages.org with your questions. Thanks! debbie Edited 13 Jun, 2023 12:52 1.01Mb

Link to this post | posted 06 Jun, 2023 01:20
debbie	I agree it is not enough yet. but good to make the post. debbie

Link to this post | posted 04 Jun, 2023 17:18
debbie	Dan, What kind of images? Do you mean the plaque or EM pic on phagesDB or something else? debbie

Link to this post | posted 02 Jun, 2023 00:26
debbie	Fred, the program needs to update to get to the right version for setting preferences. if the progam isn't avilable at cobamide…. Go the DNA master page on phagesDB. Click on the word "here" in the second sentence to download the install program. debbie

Link to this post | posted 01 Jun, 2023 02:18
debbie	Hi Martin, Are you on a mac or pc? Do you have excel? iI you do not, uncheck the load into excel box and see if that works. if not, send your .dnam5 files to me. debbie

Link to this post | posted 01 Jun, 2023 01:54
debbie	Hi Martin, The final file is a correctly formatted .dnam5 file. It is not a "profile". What file are you working with? Here is the final file submission instructions. https://seaphagesbioinformatics.helpdocsonline.com/article-49 Once I know what you are working with i ca help more. debbie

Link to this post | posted 31 May, 2023 22:31
debbie	What you did was not wrong. It is good we do things different, though it may seem confusing. I look for the most basic structural genes in every phage and when I am missing what I expect to find, I just look elsewhere. debbie

Link to this post | posted 31 May, 2023 22:01
debbie	Hi Dane, Sorry for the delay in this response. I WOULD call this a capsid maturation protease because of the hit to the UniProt hit to gp 15 in D29. Probability and Evalue is great and these gene functions were assigned by Drs. Hatfull and Hendrix back in the day. It is also in the right place and is involved in capsid assembly. debbie. BTW, i hit no MuF proteins. debbie

Link to this post | posted 30 May, 2023 13:00
debbie	Fred, I would think that the hits to the Bacillus and E.coli phages are just as compelling. I would call this a minor tail protein. debbie