SEA-PHAGES | All posts created by cdshaffer

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Link to this post \| posted 19 Jun, 2025 20:29
cdshaffer	As of 2020 there is a new rule, you should have a lysin B if you are annotating a lysin A. If you cannot find a lysin B just annotate endolysin. See this discussion: https://seaphages.org/forums/topic/4656/

Posted in: Cluster AM Annotation Tips → lysin A

Link to this post \| posted 18 Jun, 2025 21:18
cdshaffer	There is a protein in this cluster which has been annotated with two different functions: deoxycytidylate deaminase and nucleoside deoxyribosyltransferase. Check the pham for this protein: PhluffyCoco_CDS_54. These two enzymes appear to be related and have an ancient common ancestor but these two enzyme activities are quite different. Be wary of BLAST alignments for this function and focus on the top HHPRED alignments or 3D predictions. For several phages in the BS cluster the HHPRED evidence is clear these are nucleoside deoxyribosyltransferase.

Link to this post | posted 18 Jun, 2025 21:18

cdshaffer

There is a protein in this cluster which has been annotated with two different functions: deoxycytidylate deaminase and nucleoside deoxyribosyltransferase. Check the pham for this protein: PhluffyCoco_CDS_54.

These two enzymes appear to be related and have an ancient common ancestor but these two enzyme activities are quite different. Be wary of BLAST alignments for this function and focus on the top HHPRED alignments or 3D predictions. For several phages in the BS cluster the HHPRED evidence is clear these are nucleoside deoxyribosyltransferase.

Posted in: Cluster AS Annotation Tips → deoxycytidylate deaminase OR nucleoside deoxyribosyltransferase.

Link to this post \| posted 17 Jun, 2025 15:41
cdshaffer	for more discussion on this matter see this discussion: https://seaphages.org/forums/topic/5775/

Posted in: Cluster AS Annotation Tips → Terminase, small subunit in right arm

Link to this post \| posted 14 Jun, 2025 01:53
cdshaffer	Database 597 was released with 15 new phage. The whole starterator reports for these phage have been added to collection found here: https://wustl.box.com/v/Actino-phage New Phage released in 602: Chaewon DaRealMyers Ding FremontTroll Labradorite Mikronejon Montavir Peridot RegnumDei Sangak SassyC SuperSonics Trice Virizion Zarafa

Posted in: Starterator → Whole phage starterator reports

Link to this post \| posted 03 Jun, 2025 17:18
cdshaffer	We had a recent putative RecA that had some curious results so am following up on the "How to call a RecA". Our protein had what appeared to be two significant differences to the standard model. One of the hydrolytic residues did not appear to be present and the C-terminal Mg binding domain was totally missing. See the attached for more details but the final result was that our protein was still a RecA once we investigated, and shows the limits of HHPRED and the idea that anything conserved is necessary for activity. 953Kb

Link to this post | posted 03 Jun, 2025 17:18

cdshaffer

We had a recent putative RecA that had some curious results so am following up on the "How to call a RecA". Our protein had what appeared to be two significant differences to the standard model. One of the hydrolytic residues did not appear to be present and the C-terminal Mg binding domain was totally missing. See the attached for more details but the final result was that our protein was still a RecA once we investigated, and shows the limits of HHPRED and the idea that anything conserved is necessary for activity.

Posted in: SMART Function Investigations → RecA requirements

Link to this post \| posted 02 Jun, 2025 15:48
cdshaffer	Phage genomes are circular when inside the bacteria, and there are different mechanisms of how the phage goes from a linear genome in the phage particle to the circular form. Depending on the mechanism the genome assembly program may not be able to recognize the physical end of the genome and put it at base 1 of the assembly. If this happens base 1 will be somewhere in the middle of the contig. Thus for all phage you have to inspect the assembly and "rotate" it if necessary to get to the publishable form of the sequence. This is done on a case-by-case basis, and is almost always needed, however, sometimes it is not. So for a paper you need to know specifically for your phage, so best to email Dan directly and ask.

Link to this post | posted 02 Jun, 2025 15:48

cdshaffer

Phage genomes are circular when inside the bacteria, and there are different mechanisms of how the phage goes from a linear genome in the phage particle to the circular form. Depending on the mechanism the genome assembly program may not be able to recognize the physical end of the genome and put it at base 1 of the assembly. If this happens base 1 will be somewhere in the middle of the contig. Thus for all phage you have to inspect the assembly and "rotate" it if necessary to get to the publishable form of the sequence. This is done on a case-by-case basis, and is almost always needed, however, sometimes it is not. So for a paper you need to know specifically for your phage, so best to email Dan directly and ask.

Posted in: Newbler → Getting Started with Phage Assembly

Link to this post \| posted 13 May, 2025 15:02
cdshaffer	yes. The genome is going to circularize after entry, at which point there is only one copy of the repeat within the genome. This means that annotations of the linear genome will always have the possibility of this kind of quirk. In addition, if you annotated a partial gene at the start of the genome it would cause all kinds of issues for the all the computational checks and make handling the genome much more labor intensive, so the best approach is as you suggest. Annotate the copy that is the full intact gene at the end and do not annotate the partial gene at the beginning.

Link to this post | posted 13 May, 2025 15:02

cdshaffer

yes. The genome is going to circularize after entry, at which point there is only one copy of the repeat within the genome. This means that annotations of the linear genome will always have the possibility of this kind of quirk. In addition, if you annotated a partial gene at the start of the genome it would cause all kinds of issues for the all the computational checks and make handling the genome much more labor intensive, so the best approach is as you suggest. Annotate the copy that is the full intact gene at the end and do not annotate the partial gene at the beginning.

Posted in: Functional Annotation → Help with Annotating Direct Terminal Repeats

Link to this post \| posted 04 May, 2025 00:37
cdshaffer	Database 598 was released with 1 replacement phage to reflect a name spelling change. The whole starterator report for this phage has been added to collection found here just to have the correct spelling https://wustl.box.com/v/Actino-phage New Phage Released in 598: Schaffner

Posted in: Starterator → Whole phage starterator reports

Link to this post \| posted 26 Apr, 2025 18:57
cdshaffer	Database 597 was released with 1 new phage. The whole starterator report for this phage has been added to collection found here: https://wustl.box.com/v/Actino-phage New Phage Released in 594: KillerQueen

Posted in: Starterator → Whole phage starterator reports

Link to this post \| posted 19 Apr, 2025 22:54
cdshaffer	Database 596 was released with 4 new phage. The whole starterator reports for these phage have been added to collection found here: https://wustl.box.com/v/Actino-phage New Phage Released in 593: Keough Lilo27 MamaT & Skelbel

Posted in: Starterator → Whole phage starterator reports

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