Link to this post | posted 15 Oct, 2019 15:42
welkin	while not the usual case, there are a few genes through the Actinobacteriophages that are oriented as you describe. So if it is conserved throughout the cluster, go ahead and call it.

Link to this post | posted 04 Oct, 2019 13:38

welkin

Hi Amy, The only real way to tell if you have an intron is at the bench, so for the most part we do not add them to annotations. The exception being cluster J, as you noted above, where we have bench data for one in the capsid gene of LittleE and one in a minor tail gene in BAKA. So if your phages is identical in sequence to one of the two that we've demonstrated are present at the bench, you should add them. The comment about using Phamerator to find them only really works if an essential gene is split into two pieces in one phage where it is only present in one piece in the close relatives. This is how we discovered that LittleE and BAKA had introns in the first place— we knew that the capsid gene should only be one gene. So to use Phamerator, you'd need to know that genes are essential and should be only one piece— which doesn't apply to most of the phage genes as we do not know what most of them do. If you have an intron identical to one of the previously characterized ones, you can use the nucleotide sequences in Phamerator to show you exactly where the boundaries are— just get the nucleotide sequence of each gene in question and then align them against each other using BLAST.

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 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 12 Aug, 2019 18:19
welkin	Hi Steve, I think 121 is located too far away from the other called terminase gene to be a viable candidate— unless we demonstrate it at the bench. so not for now.

Link to this post | posted 16 Jul, 2019 16:50
welkin	I think if the small term or a pham with equivalent phyre predictions is present in every cluster K, it makes sense to designate both as small and large. Are there any that are missing the "small"?

Link to this post | posted 16 Jul, 2019 13:56
welkin	Hi All, Debbie and I spoke about this one, and decided to go with "antirestriction protein, OCR-like" for consistency. I do like the "DNA mimic" label– it is far more descriptive of what the protein actually does. Maybe we need to start writing some of function glossary to capture what these do. Welkin

Link to this post | posted 15 Jul, 2019 14:53
welkin	Hi Steve, We think "tellurium resistance protein D family" is the way to go. "Ter" is also the TLA for the terminase genes (which we also don't use) and we may sow confusion if we don't spell things out. Thanks!

Link to this post | posted 12 Jul, 2019 16:47
welkin	Hi! I think the first should stay as "minor tail protein" and the the second as "NKF". Tail fibers can be all sorts of sizes; they are best identified by wet bench work. Bioinformatically, they have long extended trimeric regions like triple-coiled coils or "collagen" domains.

Link to this post | posted 01 Jul, 2019 13:21
welkin	Hi All, Aragorn is back up and working. Best, Welkin