SEA-PHAGES | Gap or a gene?

Gap or a gene?

Link to this post \| posted 07 May, 2020 12:43
EWisner	I have a gene that was called in Phamerator, but not in the DNA Master autoannotation. Without it, there is about a ~300 bp gap. It is Portcullis_Draft gene 46 (36503 - 36763 ) \| pham 18840. It would be an orpham and has no sig. hits in BLAST. The coding potential in self isn't great (see attached documents). Is it a gene, or do I just have a large gap in my genome? You might notice that there is also OK coding potential in the -1 frame. I have also looked into this by blasting the a.a. sequence but it too had no sig. results. See attached documentation 192Kb

Link to this post | posted 07 May, 2020 12:43

I have a gene that was called in Phamerator, but not in the DNA Master autoannotation. Without it, there is about a ~300 bp gap. It is Portcullis_Draft gene 46 (36503 - 36763 ) | pham 18840. It would be an orpham and has no sig. hits in BLAST. The coding potential in self isn't great (see attached documents). Is it a gene, or do I just have a large gap in my genome? You might notice that there is also OK coding potential in the -1 frame. I have also looked into this by blasting the a.a. sequence but it too had no sig. results.

See attached documentation

Link to this post \| posted 08 May, 2020 02:51
debbie	Ellen, I would call this gene. There is enough coding potential for me to think it is real. It is good that you ruled out the gene in the reverse frame. debbie

Link to this post \| posted 08 May, 2020 13:44
EWisner	Thank you Debbie!

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Gap or a gene?