Link to this post | posted 09 Feb, 2021 23:26

debbie

Hi Greg, The jury is really out on all of this. We are in need of wet bench data, which is coming, but not here yet. There is just no answer at this time. I ran a comparison of the different settings and the new setting will work for now. An alternative when you run with the old settings is to parse the sequence into parts. I ran a 20kb length of a bigger genome and was able to run it at the previous setting easily. All i have for right now. Will update with additional data. a;ways check the Bioinformatics Guide for latest settings because I will keep it updated. Thanks, debbie

Link to this post | posted 06 Feb, 2021 19:05
debbie	Hi all, The site is not broken. It just won't run in any timley fashion with the settings we have been using. We did some fiddling with our settings and have modified how to run tRNA Scan SE. Go to the Bioinformatics Guide to get them!

Link to this post | posted 06 Feb, 2021 18:54
debbie	and I just revised the protocol again.

Link to this post | posted 27 Jan, 2021 19:20

debbie

Chris, Blast x takes a nucleotide sequence, translates it into all 6 reading frames and blasts. That is not needed if you want to know if the thing that was predicted by Glimmer and GeneMark has any homologues. tBlastx takes too long and would just be confusing, coding potential provides you the ORF you want to zero in on. If at any time, you think you need to look elsewhere - in another reading frame- go for it. Using nucleotide sequences to look for function homologues is not nearly as helpful as using the protein sequence. The ORFs identified by Glimmer and GeneMark (and in your auto-annoted DNA Master file) have pushed past looking for protein homologues across all 6 reading frames and showing the most likely ORF with coding potential (those are powerful and proven algorithms. Blastx of any kind is not routinely done. It can be used when you are just not convinced of what you are finding. Hope that helps, debbie

Link to this post | posted 26 Jan, 2021 00:57
debbie	Hi. I typically use the phage trained GeneMark in PECAAN, so no harm. Be sure to label the file so you know which one it is. BUT I use the host(s) trained outside of PECAAN because all can be informative, especially in the difficult to call areas. debbie Edited 26 Jan, 2021 00:58

Link to this post | posted 26 Jan, 2021 00:38
debbie	Hi Greg, I am not having trouble blasting. (I only blasted 1 gene but it completed in less than 3 minutes. I would guess that this is a server/firewall sort of problem. I would recommend restarting your computer then calling your IT folks. debbie

Link to this post | posted 25 Jan, 2021 13:23
debbie	Hi Steve, https://seaphages.org/forums/topic/224/ This link will take you to PECAAN‘s user guide. It provides directions for you to add your phage to PECAAN. Thanks, debbie

Link to this post | posted 24 Jan, 2021 12:08
debbie	Maria, without evidence, Hypothetical Protein is the best choice. thanks, debbie

Link to this post | posted 12 Jan, 2021 20:34
debbie	Andrea, That is just incorrect. Gene 21 in ActinUp is the tape measure. debbie

Link to this post | posted 08 Jan, 2021 00:33

debbie

Hi all, And remember that Holliday is named after a person, so it is one of the few words that we capitalize. "In 1964, Robin Holliday proposed a model to explain three important events that occur during meiosis in fungi: crossing-over, gene conversion, and postmeiotic segregation." (Holliday Junction Resolvases,Cold Spring Harb Perspect Biol. 2014 Sep; 6(9): a023192. doi: 10.1101/cshperspect.a023192)