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Phagesdb Entry Question

Link to this post \| posted 01 Jul, 2019 21:02
scaruso	OK, here's a dumb question. But I figure, someone needs to ask them. I have seen the "Number of Genes" field in Phagesdb where it is a total including tRNA genes and where it doesn't include tRNAs gene and, presumably reflects only protein coding genes. I would assume it is supposed to be the CDS number since at the input it says '# of ORFs' not genes, but the output says 'genes.' Can you clarify, so I know for sure? Thanks, Steve

Link to this post | posted 01 Jul, 2019 21:02

scaruso

OK, here's a dumb question. But I figure, someone needs to ask them.

I have seen the "Number of Genes" field in Phagesdb where it is a total including tRNA genes and where it doesn't include tRNAs gene and, presumably reflects only protein coding genes. I would assume it is supposed to be the CDS number since at the input it says '# of ORFs' not genes, but the output says 'genes.'

Can you clarify, so I know for sure?

Thanks,

Steve

Link to this post \| posted 02 Jul, 2019 14:16
DanRussell	Hey Steve, The intent is to have that field represent protein-coding genes only. There are separate fields for tRNAs and tmRNAs, so that info would go there. We're actually working on making these fields auto-update when we do Phamerator updates so that they're consistent and in line with Phamerator. Right now they're manually entered, so they may be less reliable. –Dan