SEA-PHAGES | Called Gene not a Gene

Link to this post \| posted today, 15:36
Wabush	There are 4 phage genes in Pham 107875 (Note: the Pham# may change by the time this is read) which may have been incorrectly added - but I am not sure about this. They are: 1) CapnMurica_51, 2) Gordon_51, 3) MiniBagel_53, and 4) Teacup_54. Regardless, the genes downstream of the above genes were deleted and should be added. Reasons for Deleting the Above Genes: ————————————- 1) GeneMarkS and GeneMark files for each of the above genes shows no coding potential - or very minimal coding potential. (see attached image MiniBagel_gp53) 2) The above annotated genes overlap a gene that was deleted. The Reasons for keeping the Deleted Downstream Gene: —————————————————- 1) The deleted gene was identified by GeneMark and Glimmer, had high coding potential, had good RBS values (see attached image Minibagel_DeletedGene), and were in a Pham with 53 other genes (see the pham for Acai_gp53 I believe the annotator may have looked at the GeneMark file instead of the GeneMarkS file when making the decision as the GeneMark file is misleading and shows no coding potential. For example: ———— the deleted MiniBagel gene from 37872-38024 has high GeneMarkS coding potential, is supported by Glimmer and GeneMark, has good RBS values: spacer 10, z-score 2.436, and final score -3.814, and is in a Pham with 53 other phage genes. In addition, by keeping this gene the following gene will have a -4 gap. Edited today, 17:18 107Kb 118Kb

Link to this post | posted today, 15:36

There are 4 phage genes in Pham 107875 (Note: the Pham# may change by the time this is read) which may have been incorrectly added - but I am not sure about this. They are: 1) CapnMurica_51, 2) Gordon_51, 3) MiniBagel_53, and 4) Teacup_54.
Regardless, the genes downstream of the above genes were deleted and should be added.

Reasons for Deleting the Above Genes:
————————————-
1) GeneMarkS and GeneMark files for each of the above genes shows no coding potential - or very minimal coding potential. (see attached image MiniBagel_gp53)
2) The above annotated genes overlap a gene that was deleted.

The Reasons for keeping the Deleted Downstream Gene:
—————————————————-
1) The deleted gene was identified by GeneMark and Glimmer, had high coding potential, had good RBS values (see attached image Minibagel_DeletedGene), and were in a Pham with 53 other genes (see the pham for Acai_gp53
I believe the annotator may have looked at the GeneMark file instead of the GeneMarkS file when making the decision as the GeneMark file is misleading and shows no coding potential.

For example:
————
the deleted MiniBagel gene from 37872-38024 has high GeneMarkS coding potential, is supported by Glimmer and GeneMark, has good RBS values: spacer 10, z-score 2.436, and final score -3.814, and is in a Pham with 53 other phage genes. In addition, by keeping this gene the following gene will have a -4 gap.

Edited today, 17:18

Link to this post \| posted today, 16:01
debbie	Hi Kieran, I agree with your assessment. debbie

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Called Gene not a Gene