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Beware Gene overcalls in this cluster
| Link to this post | posted 14 Jul, 2025 21:51 | |
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There is a region in many AS phage (typically around 18 - 23 kb) where genemark and glimmer call different genes on different strands. These genes often have very large or complete overlap. This is unusual in the extreme and finding the proper strand is a known weakness of these ab initio gene finders. As such be very suspicious of genes which overlap and are on two different strands. To call both you need very strong evidence, ideally mass spec results showing translation of both frames. However extremely high quality HHPRED hits for both potential predicted protein products might also suffice. Without extremely strong support, review the evidence and pick one gene and delete the other following the rules as outlined in the annotation guides. |
| Link to this post | posted today, 19:54 | |
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We definitely see one case fits this bill in Toad24. The original draft gene call 33, sitting the opposite strand of another gene 34, turns out to be an orphan gene, with no known similar genes in the entire PhageDB. In contrast, gene 34 have strong support. So we will NOT include this gene 33 in the final annotation. |