SEA-PHAGES | Adding genes in right arm of AS2 genomes

Adding genes in right arm of AS2 genomes

Link to this post \| posted yesterday, 22:23
seaphages_usc	I am looking at the right arm of Zhuangyuan (AS2), which has much of the right arm region not covered by auto-annotation ORF calls. In looking at the large gaps, I have found several genes with coding potential and BLAST matches, which I have added; however, there are two potential coding regions that have small blips of coding potential, but no BLAST matches. Wondering if I should call them or not. On PECAAN, they are Gene 73 (stop 38709) and Gene 76 (stop 38909). Please let me know what you think.

Link to this post | posted yesterday, 22:23

I am looking at the right arm of Zhuangyuan (AS2), which has much of the right arm region not covered by auto-annotation ORF calls. In looking at the large gaps, I have found several genes with coding potential and BLAST matches, which I have added; however, there are two potential coding regions that have small blips of coding potential, but no BLAST matches. Wondering if I should call them or not.
On PECAAN, they are Gene 73 (stop 38709) and Gene 76 (stop 38909). Please let me know what you think.

Link to this post \| posted today, 02:06
debbie	Hi all, This is where comparative genomics is helpful. Blastn the genome and you can see that right end of the genome is cobbled together and not tightly conserved across the cluster. So you won't see blastp hits for your genes. Blastn the genes in question and one has some hits and one doesn't. Put the whole picture together and the data says, the reason that no one else has called these genes is because they don't have the same sequence (38709). But gene 76 (38909 is found in LittleTokyo and Antrice. what did they call, but more importantly, look at their gen prediction data (at least GeneMark)to see if that segment has coding potential. I think you will likely want to call them, but I have not fully investigated them. Let me know if you want to chat about them. Using the comparative data should help here. Best, debbie

Link to this post | posted today, 02:06

debbie

Hi all,
This is where comparative genomics is helpful.
Blastn the genome and you can see that right end of the genome is cobbled together and not tightly conserved across the cluster. So you won't see blastp hits for your genes. Blastn the genes in question and one has some hits and one doesn't. Put the whole picture together and the data says, the reason that no one else has called these genes is because they don't have the same sequence (38709). But gene 76 (38909 is found in LittleTokyo and Antrice. what did they call, but more importantly, look at their gen prediction data (at least GeneMark)to see if that segment has coding potential.
I think you will likely want to call them, but I have not fully investigated them.
Let me know if you want to chat about them. Using the comparative data should help here.
Best,
debbie

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Adding genes in right arm of AS2 genomes