Link to this post | posted 22 Oct, 2020 00:19
afreise	Thank you so much! The Starterator split of manual annotations between sites 12 and 15 threw me off, but you make an excellent point about the better conservation of site 12. Gene 2 does appear to be real and is very well conserved in the cluster. So it looks like this one is a weird overlap!

Link to this post | posted 19 Oct, 2020 22:23

afreise

A gene early in the genome, found in A2 phages, is often called as a VIP2-like toxin OR an ADP-ribosyltransferase. The start call for this gene is very polarizing. For example, in phage Smeagan, the gene is Gene 3 (stop site 2251): Either of the two recommended start sites, 1322 or 1661, result in either a large overlap (-94) or a large gap (245). The earlier one includes a region without coding potential; the later start cuts off a lot of coding potential. The -94 start site has a slightly better RBS score and Z-score. Starterator calls for this gene are split almost down the middle between the two recommended sites, with a slight bias toward choosing the site that results in the overlap. Any guidance on this one? Thanks all! Edited 19 Oct, 2020 22:24

Link to this post | posted 26 Feb, 2020 00:53

afreise

(Sorry if this isn't the right forum - not sure where to post bioinformatics analysis questions!) We were wondering how to interpret ANI values with respect to average genome coverage/span-length of alignments. We haven't noticed any mention of this in papers which compare large numbers of phages, and would like to make sure that we are correctly interpreting high ANI values given low span-lengths. For example, some phages may share 90% ANI with span-lengths of 100%, whereas other phages may share 90% ANI with span-lengths of only 10%. While both circumstances certainly indicate some degree of sequence similarity, an ANI value of 90% seems inflated given that the aligned sequences only account for 10% of each genome. Is it appropriate to compare ANI values without regarding span-length/average coverage, or should span-length also be accounted for in our analyses?

Link to this post | posted 07 Nov, 2019 18:44
afreise	Hi Dan, Thank you so much for your reply! This clears everything up. Best, Amanda

Link to this post | posted 06 Nov, 2019 22:13

afreise

My students did a journal club on Rebekah Dedrick's D29 paper (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5712189/), and noticed when they looked D29 up on PhagesDB.org that it was listed as a temperate phage. Our understanding based on this paper and others is that D29 is lytic due to deletion of key lysogeny genes including a portion of the repressor. Could you clarify why it is designated as a temperate phage? Thank you!

Link to this post | posted 31 Oct, 2019 20:28
afreise	Hi Debbie, I can't update DrYang to be a Myoviridae in phagesdb.org because it was not our phage originally, and it is asking me to input the GPS coordinates (which I don't know) as part of the change/update.

Link to this post | posted 24 Oct, 2019 21:35
afreise	I have called this gene "major capsid and protease fusion protein" for my AU2 phage Giantsbane, since it was an acceptable function for AN arthrobacter phages (though AU phages are not listed in the official function list for this call). Confirmed here: https://seaphages.org/forums/topic/4634/

Link to this post | posted 18 Oct, 2019 18:24
afreise	Oh, interesting…We adopted DrYang from the Genome Exchange, and its PhagesDB page says it has Siphoviridae morphology (from the EM pic, I can see why - its tail looks somewhat long). But now I see that other AR phages are listed as Myoviridae. Should I update the PhagesDB page for DrYang to list it as having Myoviridae morphology based on the rest of the cluster members?

Link to this post | posted 17 Oct, 2019 22:15
afreise	Hi Welkin - just curious, did you mean phage ArV1 from this paper? I couldn't find a phage called AvR1. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5375659/ Some students are presenting the ArV1 paper for journal club. The AR cluster contractile tail on a Siphoviridae is very interesting…!

Link to this post | posted 09 May, 2018 16:15
afreise	Thank you Welkin!