Link to this post | posted 18 Aug, 2025 18:49

scaruso

Many, many thanks! In case anyone needs them: 1. Martin M. 2011. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J 17:10. 2. Jiang H, Lei R, Ding S-W, Zhu S. 2014. Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads. BMC Bioinformatics 15:182. 3. Wick RR, Judd LM, Gorrie CL, Holt KE. 2017. Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput Biol 13:e1005595. 4. Gordon D, Abajian C, Green P. 1998. Consed: a graphical tool for sequence finishing. Genome Res 8:195–202.

Link to this post | posted 03 Jul, 2025 21:07
scaruso	Lee, That is super helpful. I use PECAAN all the time, but haven't had to figure out how to use it in a class setting yet, so I am really looking forward to seeing how you went about it. Thanks again! Steve

Link to this post | posted 29 Jun, 2025 15:13
scaruso	Kristen and Lee, We have struggled on using DNAM, but I think its day's are numbered. So if you whether it is a formal or informal outline of how you use it, I would be very happy to see what you are doing as I plan for this upcomming winter and the following spring. Thanks! Steve

Link to this post | posted 03 Jul, 2024 22:34
scaruso	Many EF phages have called a gene approximately half-way in genome (by number) 2/3 into the genome (by location) RecA. There is evidence this should be called "ASCE ATPase" described in detail by Sally Molloy (University of Maine, Honors College) accessible here: https://seaphages.org/forums/topic/5567/.

Link to this post | posted 15 Mar, 2024 18:18
scaruso	Though it may no longer be relevant, SOSUI was down for a long time, but it seems to be working right now at this site: https://harrier.nagahama-i-bio.ac.jp/sosui/mobile/ Steve Edited 15 Mar, 2024 18:18

Link to this post | posted 30 Oct, 2023 01:27
scaruso	Good evening all! Does anyone have any news about Phage Enzyme Tools (PET2.0)? I have used it as part of my class for years and have noticed that it has been down for a few days. Thanks! Steve

Link to this post | posted 01 Jul, 2023 22:33

scaruso

Like in Cluster A and BD phages, the DNA primase of many cluster BF phages is split into two overlapping reading frames. The upstream portion of the gene may be missed by Glimmer and Genemark and may not be called in DNA Master. As per the entries in Cluster A and BD: "We are not sure what happens within the cell during the infection to generate the correct full length primase, so for now, we add both parts to the annotations with a large overlap."

Link to this post | posted 11 Jun, 2023 14:06
scaruso	Hello, I usually use DNAM for teaching and PECAAN for QC, but with the current DNAM connection issue, I may have to use PECAAN for teaching in a week or two in a class of 18. I can come up with something, but if I don't have to reinvent the wheel, I would rather not. So, does anyone have a way of teaching it/with it that they like and want to pass on? Thanks! Steve

Link to this post | posted 03 Jun, 2023 15:13
scaruso	Cluster BF phages have a terminase, small subunit on the right arm that has been recently identified, See RetrieverFever gp 78 Edited 03 Jun, 2023 15:14

Link to this post | posted 11 May, 2023 19:12
scaruso	Debbie, OK. Thanks! I was worried about a summer isolated Bt phage and that I was getting a warning. I will keep on keeping on if we do anymore. Though we annotate Strep in the summer, too. Thanks! Steve