Link to this post | posted 11 Sep, 2019 13:45
byrumc@cofc.edu	My class is currently annotating an adopted genome and when I produced the GeneMark(smeg)file, I noticed that many of the genes have ORFs in alternate reading frames. This happens 36 times in a genome with 90 genes. We're annotating the genes that have been called in these cases, but it seems much more common than in previous genomes that I've annotated. Should I be concerned?

Link to this post | posted 11 Sep, 2019 14:02
welkin	Hi Christine, I moved your thread to "gene or not a gene" because it is not really a question about using PECAAN but more about how to use GeneMark data to determine the gene content of your annotation. In order to give you the best answer, we need some more information— which phage is it? Could you please provide the GeneMark output you are looking at here? Thanks so much! Welkin

Link to this post | posted 11 Sep, 2019 14:55
byrumc@cofc.edu	Hi Welkin, We're looking at LastJedi. I've attached the GeneMark(smog) output. Thanks! Christine 178Kb

Link to this post | posted 11 Sep, 2019 14:55
byrumc@cofc.edu	GeneMark(smeg)

Link to this post | posted 11 Sep, 2019 18:13
welkin	Hi Christine, Do you mean changing transcription direction? Or just existing in different reading frames? The most common arrangement of genes that we see in phage genomes is a 4bp overlap, which leads to adjacent genes in different translational frames. So yes, that is quite common.

Link to this post | posted 11 Sep, 2019 19:22
byrumc@cofc.edu	I was asking about multiple genes existing in different reading frames at the same time…based on the GeneMark(smeg) calls.

Link to this post | posted 11 Sep, 2019 19:22
byrumc@cofc.edu	I was asking about multiple genes existing in different reading frames at the same time…based on the GeneMark(smeg) calls.