Link to this post | posted 16 May, 2023 16:44
plconnerly	Thank you so much, Chris! That's really helpful. We got those starterator pham numbers from PhagesDB. It looks like phamerator and starterator are both on the updated 512 version, but that the starterator links in PhagesDB are directing to the 510 version starterator pham numbers. From what you've described we can workaround by adjusting the URLs. Thanks again!

Link to this post | posted 16 May, 2023 14:32

plconnerly

Hello, We are annotating Vordorf and have found two features so far, 5 (stop at 4282) and 21 (stop at 18380), that are each in phams with many members (so not orphams), but are each not found in Starterator. When I checked versions, both Phamerator and Starterator are on version 512, but the pham numbers for these features are different in phamerator and starterator (feature 5 is in pham 80704 in phamerator, but 78088 in starterator; feature 21 is in pham 80706 in phamerator, but 78092 in starterator). Is this a situation where we just need to wait for starterator to catch up, or is there perhaps something else going on? The fact that the version numbers match is throwing me off. Thanks! Pam

Link to this post | posted 01 May, 2023 13:14
plconnerly	Thanks, Debbie! It's reassuring to know that both are okay. And it's helpful to know that it relates to the automation. Best, Pam

Link to this post | posted 01 May, 2023 02:44

plconnerly

In the Official Function list, most functions are listed in lower case, but "Hypothetical Protein" is listed with both words capitalized. I see the note that capitalization matters (#4), but is is killing me to have "Hypothetical Protein" capitalized when only specific names (RecA, DNA, Holliday, etc.) are generally capitalized in the list. It just does not match! (I do also note the exceptions of Metalloprotase and Metallophosphatase, which I haven't yet used.) Will my annotation get rejected if I use "hypothetical protein" instead?

Link to this post | posted 09 Nov, 2022 21:13
plconnerly	Vic - we're using all samples with a titer of at least 1 x 10^9.

Link to this post | posted 09 Nov, 2022 19:41

plconnerly

We could use any and all advice about DNA extraction from Gordonia rubripertincta phages. Last year we tried and troubleshot the Wizard DNA Cleanup kit column method with no success. We did phenol:chloroform:isoamyl alcohol as a last resort and managed to get useable DNA from 1 phage. This year we're trying the ZnCl2 method and initial runs have not worked. We've got some troubleshooting planed and one idea we have is to leave out the initial nuclease step. Is that allowed? Have other folks tried that? Can DNA extracted without nuclease treatment be used for sequencing? Thanks! Pam - IU Southeast

Link to this post | posted 25 Apr, 2022 19:35

plconnerly

Thanks, Debbie! I went ahead and tried both on a small set of proteins and found an interesting difference. This preprint https://doi.org/10.1101/2022.04.08.487609 about Deep TMHMM mentions issues with signal sequences being erroneously called as transmembrane domains. Although TMHMM 2.0 and Deep TMHMM agreed on their predictions for 6 of 7 proteins tested from Gordonia phage Survivors, for 1 of them TMHMM 2.0 called 1 TM domain, but Deep TMHMM indicated that region was a signal sequence, so called 0 TM domains. (We won't annotate that one as a membrane protein.) I'm not sure how to evaluate the quality of the different TM predictors - at some point, it might be worth having an more guidance on that. Pam

Link to this post | posted 25 Apr, 2022 19:04
plconnerly	The TMHMM 2.0 page linked from the Bioinformatics Guide contains a note at the top stating the TMHMM 2.0 is outdated and giving a link to Deep TMHMM (https://dtu.biolib.com/DeepTMHMM). Is either version ok for searching for transmembrane domains for calling membrane functions, or should we stick to TMHMM 2.0 because it is specified in the guide? Thanks!

Link to this post | posted 30 Mar, 2022 18:33

plconnerly

What do people recommend for taking good images of plaques on petri dishes? We usually get by with cell phone images taken by holding the plates up to the light, but I would like a more uniform and professional method. Our department may be replacing our agarose gel documentation system soon and I'm wondering if anyone has a documentation system that works well for both gels and photos of plaques. Thanks! Pam Connerly, Indiana University Southeast