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Recent Activity
Potential Gene in Pochacco
| Link to this post | posted yesterday, 22:17 | |
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Hello, We are working on annotating phage Pochaccho (Cluster GK) and we're uncertain as to whether we should keep a gene call made by Glimmer but not GeneMark. Glimmer predicts a gene starting at 16,587 to 16,730. This would give an overlap of 8 nucleotides with the previous gene and a total size of 111 bp. Given that it is less than 120 bp we were about to delete it but there's coding potential and DeepTMHMM shows that there's a transmembrane domain present is there a chance that this is a potential real gene? The gene is an orpham so there's nothing else we can compare it to. Thank you for your advice. |
17Kb| Link to this post | posted today, 01:28 | |
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Hi Arturo, It is an orpham, but that is ok. Better than ok. You are working on a phage that is the second member of cluster. So careful, de novo inspection (meaning, don't rely on what was called in the first genome, but make your best calls that you can yourselves.) and then enjoy when you come to same conclusions for same/similar genes and celebrate when you find a gene - like this one – that no other genome in our database has! (Remember to blastN it!). And i would call it a membrane protein |
| Link to this post | posted today, 06:09 | |
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Hi Debbie, Thank you for your feedback, much appreciated! We are currently annotating both phages assigned to Cluster GK, the region of the Pochacco genome where this orpham is located is slightly different to that of Smelly. We did a blastN for this gene in both phagesdb and NCBI and no significant similarity was found so it is truly unique, at least for now. Arturo |