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Recent Activity
All posts created by delesall
| Link to this post | posted 19 Dec, 2023 19:43 | |
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It also looks like the first 18 aa correspond to the beginning of Malithi gp 54, a 262 aa sequence. So maybe some HGT in ancestor of Sonah interrupted/broke this gene? |
Posted in: Gene or not a Gene → Gene or no gene at Subcluster P1 phage Sonah position 37305-37388 bp?
| Link to this post | posted 11 Jun, 2023 22:20 | |
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Some Cluster B3 and B4 phages have an intein in the middle of their terminase gene. To learn about inteins see this paper: Kelley DS, Lennon CW; SEA-PHAGES; Belfort M, Novikova O. Mycobacteriophages as Incubators for Intein Dissemination and Evolution. mBio. 2016 Oct 4;7(5):e01537-16. doi: 10.1128/mBio.01537-16. PMID: 27703073; PMCID: PMC5050341. To visualize an example of terminase with or without an intein, create a phamerator map with phage Kronus and Casbah (both B3). Note that presence of an intern may lead to identical proteins being assigned to different phams. |
Posted in: Cluster B Annotation Tips → Intein in the terminase
| Link to this post | posted 23 Mar, 2023 11:54 | |
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Does anybody know what a "Socket Error #11002" mean? Thanks |
Posted in: DNA Master → DNA Master errors
| Link to this post | posted 16 Mar, 2023 23:44 | |
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I'll add my two cents to what Chris wrote. I ended up NOT calling this a helicase loader in Rofo, mostly because there was no evidence for a helicase near by. In SPP1 and related phages, the pattern is helicase loader followed by helicae! |
| Link to this post | posted 10 Sep, 2022 13:24 | |
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Hi Nikki Yes. It magically started working again the next day (Aug 2). I did nothing different. I also just blasted one gene with no issue! Good luck, V |
Posted in: DNA Master → DNAMaster BLAST failure
| Link to this post | posted 01 Aug, 2022 20:28 | |
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I did a whole genome BLASTp within DNAMaster last week - no problem. Today DNAMaster does not seem to connect to NCBI. I have all the right permissions. Anybody else with this issue? |
Posted in: DNA Master → DNAMaster BLAST failure
| Link to this post | posted 01 Aug, 2022 17:56 | |
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I did a whole genome BLASTp within DNAMaster last week - no problem. Today DNAMaster does not seem to connect to NCBI. I have all the right permissions. Anybody else with this issue? |
Posted in: DNA Master → DNAMaster BLAST failure
| Link to this post | posted 08 Jun, 2022 00:42 | |
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Note that BE phages have a large number of tRNA genes (>40) and a tmRNA gene. Not all tRNA genes will be called by Aragorn within DNAMaster, so it is crucial to run web-based Aragorn and tRNA scan to identify all tRNA genes as well as the tmRNA. |
Posted in: Cluster BE Annotation Tips → tRNA and tmRNA genes
| Link to this post | posted 05 Apr, 2022 19:28 | |
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This forum post may be useful https://seaphages.org/forums/topic/4347/ Cheers |
Posted in: Choosing Start Sites → Cluster G1 Gene Start
| Link to this post | posted 17 Feb, 2020 03:38 | |
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If I understand your question, you want to know what MA stands for! MA = manual annotation (an annotation that has been reviewed by a human being as opposed to an auto-annotation). So for this gene, the auto-annotation has picked the start at base 1 (which is the 23rd start in this pham). When genes in this pham have been reviewed, start 23 at base 1 was picked in 190 manual annotations, while start 25 at base 10 has only 5 manual annotations. You may still want to look at CP data to see if this choice was best! Hope this helps! |
Posted in: Starterator → Starterator Documentation