SEA-PHAGES | All posts created by akoga

Link to this post \| posted 29 Mar, 2017 18:39
akoga	Becky, I looked at this same region in asapag a few days ago. While our auto-annotation did not call the genes in such a grossly overlapping way, we were still thinking we should delete the same reverse gene (44 for us) as you have decided to delete. It has NO coding potential and results in an overlap of the forward and reverse gene starts. Like yours, our next gene is a forward gene, which had Start #2 called. It looks like all the DN drafts have the earlier start conserved as well (longest ORF). For us, that is a TTG with a decent SD score. Did you decide to extend that forward gene by using the first start?

Link to this post | posted 29 Mar, 2017 18:39

Becky,
I looked at this same region in asapag a few days ago. While our auto-annotation did not call the genes in such a grossly overlapping way, we were still thinking we should delete the same reverse gene (44 for us) as you have decided to delete. It has NO coding potential and results in an overlap of the forward and reverse gene starts. Like yours, our next gene is a forward gene, which had Start #2 called. It looks like all the DN drafts have the earlier start conserved as well (longest ORF). For us, that is a TTG with a decent SD score. Did you decide to extend that forward gene by using the first start?

Posted in: Gene or not a Gene → Forward gene with good evidence among reverse genes

Link to this post \| posted 13 Mar, 2017 20:30
akoga	We are working on our genome called asapag, which is one of a few founding members of Cluster DN (Gordonia phage). We have just gotten to an area that I’m struggling with. Glimmer calls two little forward genes, one of which is also called by GeneMark. They are Genes 36 (28776-28910) and 37 (28975-29097). The next gene called is a reverse gene. There is not much coding potential for Genes 36 and 37, but there is great coding potential in that area in the reverse direction (even though neither glimmer or GeneMark call a reverse gene here). I tried creating a reverse gene (29588-28416) and I get a great Blast hit to gp 30 from Schwabeltier. However, creating this gene would cause a 90 bp overlap with the previous forward gene and has a poor SD score. In looking at Schwabeltier gp 30, it looks as though it also has a 90 bp overlap with its previous gene 29. One other note: 2 other drafts, Horus and Getalong have the first gene also (100% identical) and Getalong also has the second gene at 100% identical. It seems like I should delete the two forward genes and replace with the reverse gene, but is a 90 bp overlap too crazy?

Link to this post | posted 13 Mar, 2017 20:30

akoga

We are working on our genome called asapag, which is one of a few founding members of Cluster DN (Gordonia phage). We have just gotten to an area that I’m struggling with. Glimmer calls two little forward genes, one of which is also called by GeneMark. They are Genes 36 (28776-28910) and 37 (28975-29097). The next gene called is a reverse gene. There is not much coding potential for Genes 36 and 37, but there is great coding potential in that area in the reverse direction (even though neither glimmer or GeneMark call a reverse gene here). I tried creating a reverse gene (29588-28416) and I get a great Blast hit to gp 30 from Schwabeltier. However, creating this gene would cause a 90 bp overlap with the previous forward gene and has a poor SD score. In looking at Schwabeltier gp 30, it looks as though it also has a 90 bp overlap with its previous gene 29. One other note: 2 other drafts, Horus and Getalong have the first gene also (100% identical) and Getalong also has the second gene at 100% identical. It seems like I should delete the two forward genes and replace with the reverse gene, but is a 90 bp overlap too crazy?

Posted in: Gene or not a Gene → 90 bp overlap between forward and reverse genes

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