SEA-PHAGES | Phage DB and DNA Master number of genes mismatch

Link to this post \| posted 31 Mar, 2022 20:34
Schaudhary	Hello, we want some help as to how to go about with the number of genes not matching in DNA Master after auto-annotation and Phage DB. The DNA Master report 74 and Phage DB reports 72 genes. Gene 1 in PECAAN is forward where as in the Phage db and DNA Master is reverse. Any advice…

Link to this post \| posted 01 Apr, 2022 19:45
debbie	Hi Shima, Each time Glimmer and GeneMark predict coding potential, they use a SAMPLE of the genome to create their profiles. So the output that is then displayed in Phamerator and DNA Master can be different because data was generated independently. In my world, that is a good thing. The math of Glimmer and GeneMark breaks down for small open reading frames, and requires personal attention. (It is why we do what we do.) The outputs are showing you that a human is going to have to discern where the gene is and support that call with the data in total. It is also why I use the STOP codon of an open reading frame to identify a gene, because all others numbers can be different. debbie

Link to this post | posted 01 Apr, 2022 19:45

debbie

Hi Shima,
Each time Glimmer and GeneMark predict coding potential, they use a SAMPLE of the genome to create their profiles. So the output that is then displayed in Phamerator and DNA Master can be different because data was generated independently. In my world, that is a good thing. The math of Glimmer and GeneMark breaks down for small open reading frames, and requires personal attention. (It is why we do what we do.) The outputs are showing you that a human is going to have to discern where the gene is and support that call with the data in total.
It is also why I use the STOP codon of an open reading frame to identify a gene, because all others numbers can be different.
debbie

Link to this post \| posted 04 Apr, 2022 03:39
Schaudhary	debbie Hi Shima, Each time Glimmer and GeneMark predict coding potential, they use a SAMPLE of the genome to create their profiles. So the output that is then displayed in Phamerator and DNA Master can be different because data was generated independently. In my world, that is a good thing. The math of Glimmer and GeneMark breaks down for small open reading frames, and requires personal attention. (It is why we do what we do.) The outputs are showing you that a human is going to have to discern where the gene is and support that call with the data in total. It is also why I use the STOP codon of an open reading frame to identify a gene, because all others numbers can be different. debbie Hello Debbie, thank you for the clarification. We will keep the stop codon of ORF to compare the gene.

Link to this post | posted 04 Apr, 2022 03:39

Schaudhary

debbie
Hi Shima,
Each time Glimmer and GeneMark predict coding potential, they use a SAMPLE of the genome to create their profiles. So the output that is then displayed in Phamerator and DNA Master can be different because data was generated independently. In my world, that is a good thing. The math of Glimmer and GeneMark breaks down for small open reading frames, and requires personal attention. (It is why we do what we do.) The outputs are showing you that a human is going to have to discern where the gene is and support that call with the data in total.
It is also why I use the STOP codon of an open reading frame to identify a gene, because all others numbers can be different.
debbie

Hello Debbie, thank you for the clarification. We will keep the stop codon of ORF to compare the gene.

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Phage DB and DNA Master number of genes mismatch