Link to this post | posted 16 Aug, 2019 22:54
DrHHNZ	Thanks Claire, That is helpful and we had seen some hints in the HHpred. The students had suggested that the only matches were all "integrases" without any further designation. I will have to take a closer look when we are back in class again. Thanks again for your time! Best, Heather

Link to this post | posted 17 Aug, 2019 20:12

lhughes

DrHHNZ Thanks Claire, That is helpful and we had seen some hints in the HHpred. The students had suggested that the only matches were all "integrases" without any further designation. I will have to take a closer look when we are back in class again. Thanks again for your time! Best, Heather Hi Heather - I think that is an NCBI issue. The hits used to say which they were, but I think more recently NCBI decided to use the generic "integrase" for everything so that information doesn't pop out like it used to. Lee

Link to this post | posted 18 Aug, 2019 20:03
scaruso	I see you added Topcons now, too. Cool! Steve

Link to this post | posted 26 Jan, 2020 14:53

delesall

Is there a document explaining how to interpret Topcons data? I looked around the SEA-PHAGES forums, the Bioinformatics guide and found nothing. The Topcons paper is a little dense for me. In particular I'm QC.ing AwesomeSauce - an F1 which is in Pecaan. In that phage, gene 33 (start 28413) has that HHPred match to the Putative lactococcus lactis phage r1t holin which has no transmembrane domain when run through TmHmm. The Topcons summary shows different results depending on the program but the reliability box shows nothing (which is different from the easier to interpret membrane protein for gene 29 in this phage). I interpreted this as no evidence for a transmembrane domain and would thus not call this the holin. Any insight on how to interpret teh Topcons summary for this gene would be appreciated!

Link to this post | posted 29 Jan, 2020 03:40

ClaireRinehart

TOPCONS has a very good prediction statistics compared to other prediction programs, including TmHmm. The five supporting methods, shown along with TOPCONS, aid in developing the reliability score graphic. To score high on reliability you need to have a TM domain predicted by TOPCONS and all of the other five supporting programs at the same location. The neat thing about TOPCONS is its ability to accurately predict when there is no TM domain. TOPCONS is over 95% accurate in predicting when there is no TM domain. So, if there is no TM domain found in the TOPCONS line then you can bet that it is not a membrane protein. I looked at gene 34 (start 28413) in PECAAN and see TOPCONS evidence for two TM domains, which fits the two TM domain evidence for the phage r1t holin. At least one domain has decent support from three out of five of the other prediction programs, which is OK support. I think that there is enough evidence for the holin call. Claire

Link to this post | posted 15 May, 2024 16:19
cellokiwi	Hi Claire, I am having an issue where Aragorn is calling A BUNCH of tRNAs when I manually enter the FASTA and PECAAN is calling none of them. I went to put them in with the "Add a gene" button but it only lets me put in stop coordinates, not start. What am I missing? Thanks!

Link to this post | posted 20 May, 2024 14:57

ClaireRinehart

You can't enter un-called tRNAs into PECAAN. Sorry. You can get PECAAN to rerun the tRNA and tmRNA search by clicking on the Admin menu button and then selecting the Phage option. Next enter the name of your phage into the search box and once you see your phage, click on the Edit button at the right hand edge of your phage line. You will then be given the option to 'Rerun the tRNA and tmRNA' search.