Link to this post | posted 06 Aug, 2020 15:34
debbie	Steve, This has just been revised. Check out the Pre-Qo pathway case study just posted in the Bioinformatics Guide. The revised functional assignments are listed on the approved functions Google doc. August 6, 2020.

Link to this post | posted 06 Aug, 2020 15:25
debbie	This has been revised a bit, please check the approved Function Assignment list (Google doc) and the Pre Qo pathway Case Study in the Bioinformatics Guide. August 6, 2020.

Link to this post | posted 28 Jul, 2020 21:34

debbie

It seems we keep hitting the PE/PPE proteins that are only and easily found in the Mycobacteria. Rather than avoid calling them because they can be part of functions that are not yet identified, let's start adding PE/PPE family proteins to the annotations. The attached document provides useful information to what to look for when deciding if your protein of interest has all of the necessary parts. It also includes a citation for a paper for reference. A good example is Kayacho_gene 88 (Cluster B6). However, these proteins are found in lots of phage genomes, so not a cluster specific topic. debbie 7-28-20 Edited 28 Jul, 2020 21:37 115Kb

Link to this post | posted 13 Jul, 2020 21:14
debbie	Amaya, Nope. No cutoff score per se, but bigger is better. I think I only look at top hits or areas of interest. But your approach is the one that sounds reasonable. It has to make sense. debbie

Link to this post | posted 13 Jul, 2020 20:29
debbie	Claire, I sent this on to Graham. Because of the hit and significance to T4, he is incline to call this gene "Imm-like superinfection immunity protein". Please call it in your current genome. I added it to the approved functions list. Edited 15 Jul, 2020 20:32

Link to this post | posted 09 Jul, 2020 14:08
debbie	Some folks have been receiving SSL errors when trying to download GenBank files from GenBank. Jackie Washington provide a solution. The fix is to download the C++ Visual package from https://www.microsoft.com/en-us/download/details.aspx?id=5555 and restart. Shen she did that, the problem corrected. debbie Edited 09 Jul, 2020 14:10

Link to this post | posted 27 Jun, 2020 13:48

debbie

Claire, The Starterator data for the shorter start is quite compelling. I just looked at a different scenario where the -4bp overlap was on a portal gene. In this case, the thought was that the structural studies for the portal protein out-weighed the convenient -4bp overlap. In this case -with such a tiny gene and in a place where the -4bp overlap is common - I can't blame you for picking it. We need experiments! About your 'evolving pham' comment, maybe this is an older version…… debbie

Link to this post | posted 24 Jun, 2020 13:54
debbie	In fact, there are no hits to tail assembly chaperones proteins in DH, so for now, we are not going to call them at all.

Link to this post | posted 23 Jun, 2020 23:51
debbie	Let me know how it goes!

Link to this post | posted 23 Jun, 2020 23:29

debbie

Do you a complete set of documentation in one of your files? Copy it from whatever corrupted file it is in and paste it into the (empty) documentation of a perfect sequence file. (To get that sequence file, open a .fasta and stop before you auto-annotate.) Then parse. You won't have blast data, but you also won't have to re-enter as much. You can cut and paste from multiple files. Sorry I can't do better.