SEA-PHAGES | wrap around genes in C1

Link to this post \| posted 25 Aug, 2017 23:20
jparker	Hello, The Cluster C1 phages I have been annotating are circularly permuted and have a gene that appears to wrap around the end of the genome. Is there anything else that needs to be done when annotating these? I'm assuming it should be changed to "CDS" from "misc_signal"? This is what it looks like in the documentation: misc_signal join(155400. .155759;1. .1 /gene="259" /product="gp259" /locus tag="KOGUMA_259" Thanks! Jordan

Link to this post | posted 25 Aug, 2017 23:20

Hello,
The Cluster C1 phages I have been annotating are circularly permuted and have a gene that appears to wrap around the end of the genome. Is there anything else that needs to be done when annotating these? I'm assuming it should be changed to "CDS" from "misc_signal"?

This is what it looks like in the documentation:
misc_signal join(155400. .155759;1. .1 smile

/gene="259"
/product="gp259"
/locus tag="KOGUMA_259"

Thanks!
Jordan

Link to this post \| posted 27 Aug, 2017 15:25
kklyczek	Hi Jordan, I am also reviewing C1 phages and was wondering about this. In GenBank the wraparound genes are labeled as "misc_feature" but that is not a menu option in DNA Master. I think "misc_signal" is something different? I checked a few C1 phages submitted recently and the DNAM files label the wraparound genes as "cds" with 2 regions, sometimes with an explanation in the Notes window. GenBank must add the "misc_features" tag? This is what is looks like in the final documentation: CDS join(154634. .155205;1. .4) /gene="271" /product="Hypothetical Protein" /locus tag="SEA_AUDRICK_271" /note=circularly permuted genome; selection of sequence origin for linear molecule results in coding region disruption Karen

Link to this post | posted 27 Aug, 2017 15:25

kklyczek

Hi Jordan,

I am also reviewing C1 phages and was wondering about this. In GenBank the wraparound genes are labeled as "misc_feature" but that is not a menu option in DNA Master. I think "misc_signal" is something different? I checked a few C1 phages submitted recently and the DNAM files label the wraparound genes as "cds" with 2 regions, sometimes with an explanation in the Notes window. GenBank must add the "misc_features" tag?

This is what is looks like in the final documentation:
CDS join(154634. .155205;1. .4)
/gene="271"
/product="Hypothetical Protein"
/locus tag="SEA_AUDRICK_271"
/note=circularly permuted genome; selection of sequence origin for linear molecule results in coding region disruption

Karen

Link to this post \| posted 17 Jul, 2018 19:56
clfleischacker	Is the last, wrap-around gene an assumed gene for C1 cluster phages? I deleted it earlier in my annotation but need to know if I should add it back in. Chris

Link to this post \| posted 17 Jul, 2018 20:38
clfleischacker	I followed the advice from Karen above but the validation now says incorrect length for this gene. I have pressed the calculator button, etc. with no changes. Any other suggestions?

Link to this post \| posted 08 Jun, 2024 18:47
mpedulla	Many C1 Cluster genomes contain a protein-coding gene that spans across from the right end to the left end of the genome; however, they are not consistently called and are not displayed in Phamerator.

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wrap around genes in C1