Link to this post | posted 04 Mar, 2020 17:31
debbie	Maria, I just took your file and generated a GenBank file with no errors. Did you choose the "Bacteria and Plant Plastid Code" on the Description pane of Submit to GenBank? all of the genes you have errors for have GTG starts (I think). debbie

Link to this post | posted 03 Mar, 2020 17:50

debbie

Hi all, I am going to chime in here, but my understanding today is that every phage may not have the G/T programmed frameshift. In lots of cases we can only find homologues to G and nothing to T. If the downstream gene of the frameshift does not have homologues and you cannot find a slippery sequence as denoted in the review paper cited in the guide https://seaphagesbioinformatics.helpdocsonline.com/article-54 , do not 'force' a frameshift. I would not call 4Gs, not followed by 3 of something else as a slippery sequence (though we have done it in the past). Is that the case here? debbie

Link to this post | posted 01 Mar, 2020 13:01

debbie

Hi Greg and all, Delete the 2 N's in the sequence pane of the file. Then click the "Raw" button (top right corner). I could try to tell you what "Raw" means, but I do not know the origin. What this button does is some form of reformatting to the sequence (to endure there is no 'hidden' characters) that allows the change to be posted. (Also make sure that the little 'lock' icon in the bottom right corner is 'open (unlocked). debbie

Link to this post | posted 28 Feb, 2020 02:28
debbie	Greg, Here are my best answers: Is there a way to align the two DNA sequence files to determine where the nucleotides have been added or deleted? Yes! Use the align 2 sequences at ncbi's blastn. But my best guess is that there are 2 Ns at the end of the longer sequence. i would check there first.

Link to this post | posted 19 Feb, 2020 18:05

debbie

Just looked at 2 cluster AO2 phages, JKerns and StevieBAY. StevieBAY's gene 28 is an endolysin. It possesses all of domains we expect to see in an endolysin. Gene 64 codes for the CHAP endopeptidase domain of LysK (a Staphylococcus phage lysin gene). It is reported out as an endolysin also. We won't call either of them lysin A (Reserved only for mycobacteriophages for now, unless the phage genomes contains a lysin A and a lysin B. Edited 19 Feb, 2020 18:17

Link to this post | posted 12 Feb, 2020 18:45
debbie	Deb, The file (not the program) is likely corrupted. Follow these directions in the Bioinformatics Guide. https://seaphagesbioinformatics.helpdocsonline.com/article-104 It is tedious, so be careful as you do this. If it doesn't work, send me the file. Good luck! debbie Edited 12 Feb, 2020 18:46

Link to this post | posted 05 Feb, 2020 21:09
debbie	Excellent idea! Thanks Chris!

Link to this post | posted 02 Feb, 2020 20:00
debbie	Amy, If send me the file, I will try to fix it. debbie

Link to this post | posted 30 Jan, 2020 21:16
debbie	Gene 73 of phage Krampus is best labeled as a RuvC-like resolvase. Resolvase is too general of term to use. (Determined in a conversation with G. Hatfull.

Link to this post | posted 24 Jan, 2020 20:17

debbie

In calling the immunity repressor of a phage JF2 (gp71), we came across a peculiar finding. It seems that the immunity repressor's open reading frame has less coding potential than another open reading frame in that area. Don't be fooled! JF2's immunity repressor shows hits in HHPred to the HTH DNA binding site (N-terminus). Read Pope, et al 2011a for info about Bxz2's broken repressor. However, our gene doesn't match that N terminus either. Many (did I say many?) phages have miscalled the open reading frame as the immunity repressor. Be careful. We will fix as soon as we can. debbie