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Recent Activity
All posts created by debbie
| Link to this post | posted 26 Jan, 2021 00:57 | |
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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 |
Posted in: PECAAN → GeneMarkS ?
| Link to this post | posted 26 Jan, 2021 00:38 | |
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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 | |
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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 |
Posted in: Bioinformatic Tools and Analyses → PECAAN
| Link to this post | posted 24 Jan, 2021 12:08 | |
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Maria, without evidence, Hypothetical Protein is the best choice. thanks, debbie |
Posted in: Functional Annotation → Singleton FuzzBuster Major Capsid
| Link to this post | posted 12 Jan, 2021 20:34 | |
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Andrea, That is just incorrect. Gene 21 in ActinUp is the tape measure. debbie |
Posted in: Annotation → Tape measure in K1 phage
| Link to this post | posted 08 Jan, 2021 00:33 | |
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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) |
| Link to this post | posted 05 Jan, 2021 14:10 | |
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Fernando, There are a lot of factors that impact how poorly Blast completes. It sounds like it just needs to have more time. I have waited longer than overnight to complete a blast. You can try blasting in sections. See this section of the guide. https://seaphagesbioinformatics.helpdocsonline.com/article-70 good luck! debbie |
Posted in: DNA Master → DNAMaster BLAST failure
| Link to this post | posted 30 Dec, 2020 23:44 | |
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Matt, Ok. It is never simple, is it? Good luck. debbie |
Posted in: DNA Master → DNA Master Application Corrupted
| Link to this post | posted 30 Dec, 2020 20:04 | |
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Hi Matt, This sounds like 2 different problems, both alluding to incomplete download/installation problems. I would first recommend uninstall and reinstall. Also, does the installer have admin priviledges? You are missing some files/drivers. Do you still have DNA master on your old computer? We may have to do some copy/pasting. debbie |
Posted in: DNA Master → DNA Master Application Corrupted
| Link to this post | posted 17 Dec, 2020 02:48 | |
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Dr. Catalase, Yes. Please use the validation function in DNA Master to do this when you renumber the genes. It is always best to let DNA Master auto-fill any field that you can debbie |
Posted in: Notes and Final Files → Filling in the Product field