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Recent Activity
All posts created by coomansr
| Link to this post | posted 02 Jun, 2022 21:11 | |
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Thanks Kristen! After QC working fine last week, I got this error the other day (using a PC). Your patch fixed it. Roy |
Posted in: Bioinformatic Tools and Analyses → Solution to missing MMseqs2 error for Mac version of flat file checker
| Link to this post | posted 26 May, 2021 14:52 | |
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In addition to the above RepA-like replication initiator I have a second "replisome organizer" in Samman98 (CZ4) (immediately downstream of RepA-like replication initiator). gp70 in DNAM file, gene 71 in PECAAN. Strong HHpred hit to "replisome organizer; helical bipartite natively unfolded domain, replication; HET: MSE; 2.4A {Bacillus phage SPP1} SCOP: a.179.1.1, l.1.1.1" 98.8% prob/49.3% coverage (PDB 1NO1_C). Also 99% probability/45% coverage hit to Pfam "Inhibitor_G39P ; Loader and inhibitor of phage G40P" (PF11417.9). Suggestions for function? Roy |
375KbPosted in: Request a new function on the SEA-PHAGES official list → phage replisome organizer found in Cluster T; add to Master List?
| Link to this post | posted 03 Sep, 2020 19:02 | |
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Debbie & Steve, I am also getting Error connecting with SSL. EOF was observed that violates the protocol. Roy |
Posted in: DNA Master → Blast error
| Link to this post | posted 06 Feb, 2020 15:32 | |
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Annotating Rie18_gp40. Starterator report for pham 109510 not found. Not an orpham and number appears to still be good. Roy |
Posted in: Starterator → Pham not found in Starterator
| Link to this post | posted 26 Feb, 2019 16:29 | |
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Working on Kuwabara gp90, Pham 17026, and did not find a Starterator Report. Gene present in several Cluster DN phages. Roy |
Posted in: Starterator → Pham 17026 Report Not Found
| Link to this post | posted 22 Jan, 2019 22:22 | |
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Got a Page/Report not found error for Pham 60238. 34 members and number seems current. |
Posted in: Starterator → Pham not found in Starterator
| Link to this post | posted 07 May, 2018 12:52 | |
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Got it. Thanks. |
Posted in: Starterator → Pham not found in Starterator
| Link to this post | posted 06 May, 2018 16:03 | |
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I'm working on Ali17, gp63, and can't locate a Starterator report for pham 45669. It's not an orpham and I've checked Phagesdb to make sure the pham hasn't been renumbered. |
Posted in: Starterator → Pham not found in Starterator
| Link to this post | posted 30 Mar, 2018 17:37 | |
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All: In Brylie, gp29 and gp30 correspond to the two lysin A genes. These match closely the two in BetterKatz (also 29 & 30). Is the correct annotation lysin A, protease M15 domain and lysin A, glycosyl hydrolase domain as in the approved list of functions or lysin A, N5 cysteine protease domain and lysin A, GH19 glycoside hydrolase domain, as in BetterKatz? Roy |
Posted in: Functional Annotation → Lysins in Gordonia
| Link to this post | posted 19 Feb, 2017 16:56 | |
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On occasion, when I compare called start sites between DNA Master and PECAAN, I see different results. For example, with Royals2015, in DNA Master I see "Original Glimmer call @bp 36409 has strength 8.82" but in PECAAN I see "Glimmer Start: 36409 Glimmer Score: 8.82 GeneMark Start: 36352 Starterator Start: Pham 24601". I have seen this other times, where PECAAN states different starts for GL and GM, but DNAM gives only one start (implying GM and GL agree). Have others noticed this? Anyone have an explanation? Roy |
Posted in: PECAAN → DNAM/PECAAN GeneMark calls differ?