SEA-PHAGES | All posts created by seaphages

Link to this post \| posted 01 Dec, 2025 22:23
seaphages_usc	I am looking at the right arm of Zhuangyuan (AS2), which has much of the right arm region not covered by auto-annotation ORF calls. In looking at the large gaps, I have found several genes with coding potential and BLAST matches, which I have added; however, there are two potential coding regions that have small blips of coding potential, but no BLAST matches. Wondering if I should call them or not. On PECAAN, they are Gene 73 (stop 38709) and Gene 76 (stop 38909). Please let me know what you think.

Link to this post | posted 01 Dec, 2025 22:23

I am looking at the right arm of Zhuangyuan (AS2), which has much of the right arm region not covered by auto-annotation ORF calls. In looking at the large gaps, I have found several genes with coding potential and BLAST matches, which I have added; however, there are two potential coding regions that have small blips of coding potential, but no BLAST matches. Wondering if I should call them or not.
On PECAAN, they are Gene 73 (stop 38709) and Gene 76 (stop 38909). Please let me know what you think.

Posted in: Cluster AS Annotation Tips → Adding genes in right arm of AS2 genomes

Link to this post \| posted 25 Nov, 2025 20:15
seaphages_usc	Hi, I seem to be having this issue with PECAAN in that it is not initiating BLAST searches or creating a log. Anyone else?

Posted in: PECAAN → PECAAN not BLASTing?

Link to this post \| posted 29 Dec, 2023 13:50
seaphages_usc	This works great, thank you so much for the heads up! afreise Good news! VMWare Fusion version 13.5 contains a built-in approach to installing WIndows 11 ARM version. All you have to do is install VMWare and then when the wizard pops up, select 'Get Windows from Microsoft". It will auto-download the ARM version. I used it and then downloaded DNA Master using Kristen's update package successfully. Note: when you first boot Windows, you must click within the window and press a key within 5 seconds or it will time out. (more info: https://communities.vmware.com/t5/VMware-Fusion-Discussions/Windows-11-download-not-working/td-p/2992757)

Link to this post | posted 29 Dec, 2023 13:50

seaphages_usc

This works great, thank you so much for the heads up!

afreise
Good news! VMWare Fusion version 13.5 contains a built-in approach to installing WIndows 11 ARM version. All you have to do is install VMWare and then when the wizard pops up, select 'Get Windows from Microsoft". It will auto-download the ARM version. I used it and then downloaded DNA Master using Kristen's update package successfully.
Note: when you first boot Windows, you must click within the window and press a key within 5 seconds or it will time out. (more info: https://communities.vmware.com/t5/VMware-Fusion-Discussions/Windows-11-download-not-working/td-p/2992757)

Posted in: DNA Master → DNA Master on M1 Mac

Link to this post \| posted 20 Mar, 2023 01:32
seaphages_usc	Thank you! That makes sense all around. debbie Using the phamerator numbers I would likely not call either 39 or 40. 34296 - 34397 has enough (though slight) coding potential for me to consider calling this one. No Other FF has this sequence. Note that this genome has 2 tRNAs, make sure there is not any overlap between genes/tRNAs.

Posted in: Cluster FF Annotation Tips → Tricky gaps

Link to this post \| posted 18 Mar, 2023 19:58
seaphages_usc	I am exploring two gaps in Gusanita's ORF assignment by DNA Master and am having some trouble deciding if they are good to call or not. 1) Thoughts on deleting called gene, forward, 29241-29357 as it doesn't have good BLAST data and no other related phage have a forward gene in the middle of this reverse stretch. Possible new genes: 2) 29270 start, 28890 stop, reverse orientation, has a BLAST match, but not good HHPred data. This still leaves a gap here, but I don't see any other good options and no related phage give strong comparison in this area. 3) 34296 start, 34397 stop, -4 overlap, BLAST matches look good

Link to this post | posted 18 Mar, 2023 19:58

seaphages_usc

I am exploring two gaps in Gusanita's ORF assignment by DNA Master and am having some trouble deciding if they are good to call or not.
1) Thoughts on deleting called gene, forward, 29241-29357 as it doesn't have good BLAST data and no other related phage have a forward gene in the middle of this reverse stretch.

Possible new genes:
2) 29270 start, 28890 stop, reverse orientation, has a BLAST match, but not good HHPred data. This still leaves a gap here, but I don't see any other good options and no related phage give strong comparison in this area.
3) 34296 start, 34397 stop, -4 overlap, BLAST matches look good

Posted in: Cluster FF Annotation Tips → Tricky gaps

Link to this post \| posted 18 Mar, 2023 00:07
seaphages_usc	Thank you! debbie Hi! I could call 41673-41810. There is a nib of coding potential and that if fits with 4bp overlaps at both ends is compelling. I think the coding potential is there for 41974-42225. However, I am not sure about the last one 42293-42394. I don't think that i would call it. debbie

Posted in: Cluster F Annotation Tips → 4 bp overlaps

Link to this post \| posted 17 Mar, 2023 22:50
seaphages_usc	Working on the end of Cluster FF phage Gusanita and am wondering what criteria I should use to add a gene here. I could insert a gene at start site 41673 with a -4 overlap. There is decent BLAST and HHPred matches here, so I am comfortable with that. There is potential for another gene at 41974, also with a -4 overlap. This one doesn't have good HHPred or BLAST matches. Should I leave it out or go with the notion that it's an orphan with its attractive overlap. Lastly, a potential start at 42293 with a -4 overlap and a single BLAST match. Any help would be appreciated with these gaps at the end with lovely potential ORFs. welkin The right arms of cluster F genes are characterized by TONS of tiny genes. These genes are sometimes so small that the gene prediction programs have a really difficult time predicting them. You can usually identify them easily though, as their start and stop codons will overlap with the flanking genes in a 4bp overlap.

Link to this post | posted 17 Mar, 2023 22:50

seaphages_usc

Working on the end of Cluster FF phage Gusanita and am wondering what criteria I should use to add a gene here.
I could insert a gene at start site 41673 with a -4 overlap. There is decent BLAST and HHPred matches here, so I am comfortable with that.
There is potential for another gene at 41974, also with a -4 overlap. This one doesn't have good HHPred or BLAST matches. Should I leave it out or go with the notion that it's an orphan with its attractive overlap.
Lastly, a potential start at 42293 with a -4 overlap and a single BLAST match.
Any help would be appreciated with these gaps at the end with lovely potential ORFs.

welkin
The right arms of cluster F genes are characterized by TONS of tiny genes. These genes are sometimes so small that the gene prediction programs have a really difficult time predicting them. You can usually identify them easily though, as their start and stop codons will overlap with the flanking genes in a 4bp overlap.

Posted in: Cluster F Annotation Tips → 4 bp overlaps

Link to this post \| posted 20 Jan, 2022 02:15
seaphages_usc	Hi All, I have DNA Master working on Parallels/Windows 11 on my M1 Mac. And several of my students do as well. You can download a trial copy for 14 days to give it a try. Our university has a 1-year subscription to Parallels for about $40, so I'll use some funds to buy copies for my students who need it.

Posted in: DNA Master → DNA Master on M1 Mac

Link to this post \| posted 05 Jan, 2022 19:46
seaphages_usc	Great, thank you! We'll give Parallels a try to see how it works.

Posted in: DNA Master → DNA Master on M1 Mac

Link to this post \| posted 04 Jan, 2022 21:36
seaphages_usc	Any ideas on how to run DNA Master on a new M1 Mac?

Posted in: DNA Master → DNA Master on M1 Mac

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