Welcome to the forums at seaphages.org. Please feel free to ask any questions related to the SEA-PHAGES program. Any logged-in user may post new topics and reply to existing topics. If you'd like to see a new forum created, please contact us using our form or email us at info@seaphages.org.
Recent Activity
engstrom posted in AAA ATPase or RecA recombinase?
sklambet@ncsu.edu posted in DNA Master on M1 Mac
cdshaffer posted in Whole phage starterator reports
fbaliraine posted in Phage DoRead Start at 52714 bp with 8 bp overlap vs start at 52718 with 4 bp overlap?
Debbie Jacobs-Sera posted in Phage DoRead Start at 52714 bp with 8 bp overlap vs start at 52718 with 4 bp overlap?
All posts created by debbie
| Link to this post | posted 02 Mar, 2021 22:19 | |
|---|---|
|
Hi Susanne, Yes. That is a classic presentation of a programmed frameshift found in tail assembly chaperone genes. There is some introductory info in the Bioinformatic Guide: https://seaphagesbioinformatics.helpdocsonline.com/article-54 https://seaphagesbioinformatics.helpdocsonline.com/article-6 Lots have been written about them in the literature. debbie |
Posted in: Gene or not a Gene → genes 19/20 in K1 subcluster
| Link to this post | posted 02 Mar, 2021 18:41 | |
|---|---|
|
|
The rIIA-like protein and rIIB-like protein assignments are now on the SEA-PHAGES Functional Assignments List. The significant hits are seen when using the UniProt-SwissProt-viral database at HHPred. debbie Also, this links to an excellent read on the proteins. |
Posted in: Functional Annotation → riiA and riiB like proteins
| Link to this post | posted 01 Mar, 2021 00:52 | |
|---|---|
|
|
The pfam hits to holin are not great but also not shabby. The typical order of genes is not present in the B1s, so that is also not helpful. However, it is interesting that this gene has 4 transmembrane domains, and the 2 subsequent genes each have 2 transmembrane domains. So I would be inclined to call all three "membrane proteins". |
Posted in: Cluster B Annotation Tips → Holin
| Link to this post | posted 26 Feb, 2021 19:51 | |
|---|---|
|
|
Hi Shallee, What genes are you referring to? thanks, debbie |
Posted in: Cluster B Annotation Tips → Holin
| Link to this post | posted 26 Feb, 2021 13:12 | |
|---|---|
|
|
Hi! I am not sure the evidence is convincing. I would like to investigate a bit. |
Posted in: Functional Annotation → riiA and riiB like proteins
| Link to this post | posted 20 Feb, 2021 00:04 | |
|---|---|
|
|
You're welcome! |
Posted in: Functional Annotation → PLA2-like domain in Cluster B1s
| Link to this post | posted 19 Feb, 2021 23:49 | |
|---|---|
|
|
I do not think that this protein (gene35 of Sarma624) has a reportable function. HHPred has no hits to an applicable function. |
Posted in: Functional Annotation → PLA2-like domain in Cluster B1s
| Link to this post | posted 19 Feb, 2021 01:09 | |
|---|---|
|
|
Yep. Looks like an error to me. We will get this corrected as we continue with genome curations. Thanks! debbie |
| Link to this post | posted 15 Feb, 2021 17:07 | |
|---|---|
|
|
Joe, It doesn't matter, just state (maybe in your cover letter) what you used. debbie |
Posted in: Annotation → % alignment
| Link to this post | posted 09 Feb, 2021 23:26 | |
|---|---|
|
|
Hi Greg, The jury is really out on all of this. We are in need of wet bench data, which is coming, but not here yet. There is just no answer at this time. I ran a comparison of the different settings and the new setting will work for now. An alternative when you run with the old settings is to parse the sequence into parts. I ran a 20kb length of a bigger genome and was able to run it at the previous setting easily. All i have for right now. Will update with additional data. a;ways check the Bioinformatics Guide for latest settings because I will keep it updated. Thanks, debbie |
Posted in: tRNAs → tRNAScan-SE Down-ish?