Link to this post | posted yesterday, 21:39

rdejong

We have a possible Tail Assembly Chaperone frameshift in two new cluster CF phages (CurlyFries and RegnumDei). The only possible slippery sequence is GGATTTC. In two previous CF annotations that have this same sequence (Shagrat and Madraxi), a frameshift was not called. In another CF annotation, Jflix2, the putative slippery sequence is GGGTTTC, and it was called as a frameshift. Seems like the GGATTTC, conserved in 4 phages in the cluster, could also be a slippery sequence. But without stronger evidence, better to not call it as a frameshift? Any opinions out there? Thanks! Edited 10 minutes ago

Link to this post | posted 31 Jul, 2025 22:52

rdejong

We were annotating the following protein, with hits to binding proteins and HTH domain containing proteins. MPLVKTAAEINREIRSMCPPTAPPPPPASRSDRQLGPMQYALLELVRSKPYWVVDRAFWRVMARKLRVPAWRVRKVFLSLEEGGYILVSERENPRIAQATERGRR Checking for HTH on HHpred output wasn't totally clear. In the output below, I've put green boxes around possible HTH regions for both the Query and the Target. The Target has a definite HTH domain. The Query, however, is a little doubtful. One of the helices is only 3 amino acids long, and my understanding is that at least 5 aa's are needed for a stable helix. Rick Pollenz was consulted and confirmed that there is not a HTH in that protein. He used two programs to investigate: https://users.cis.fiu.edu/~giri/bioinf/GYM2/prog.html https://npsa-prabi.ibcp.fr/cgi-bin/npsa_automat.pl?page=/NPSA/npsa_hth.html Thanks Rick! Our call is going to be DNA binding protein Edited 31 Jul, 2025 22:53 89Kb

Link to this post | posted 07 Apr, 2025 17:14
rdejong	Thanks, yes, that is the purpose. I considered that option, but found that I was able to avoid this error by doing an install on a different computer. It happens to be Windows 10 instead of Windows 11, for what it's worth. Genome submitted with reBLAST complete!

Link to this post | posted 05 Apr, 2025 13:01

rdejong

I am getting the error quoted at the bottom of this from Steve Caruso. I tried a couple of other fixes that are in the forum regarding SSL/DNA BLAST errors: the Windows library and the Bitvise SSH client. The prose regarding the Windows library fix is copied below. Since neither of these things work, any ideas? DanRussell Hi Katie, I think this error is due to not having a certain library installed on the particular version of Windows that's running. That library wasn't required until after the update earlier this year to use secure NCBI servers. I think I came across that error myself, and in my notes I have that I went to the link below and installed the Visual C++ package there, then restarted and it worked. https://www.microsoft.com/en-us/download/details.aspx?id=5555 UPDATE Sep 2021: The link above no longer works, but the file can be found at the link below now. Download it from within Windows and then run it, and make sure you close DNA Master and restart Windows before trying to BLAST again. https://phagesdb.org/static/vcredist_x86.exe Hopefully that helps, –Dan scaruso All, I am getting the following error when I try to blast a gene in DNAM on my PC running W10 (not a surface). Error connecting with SSL. error: 1409442E:SSL routines::SSL3_READ_BYTES:tlsv1 alert protocol version. Anyone else having any trouble or aware of anything going on? Or any ideas? Steve

Link to this post | posted 27 Feb, 2024 18:02

rdejong

Like fbaliraine (Fred) we have a possible minor tail protein called very early (gene 4) in our phage that is called a minor tail protein in a similar gene (JFlix 2). Unlike the previous post, we have no correlation to any gene with any canonical orientation. We ended up calling this gene minor tail protein in Jflix2 last year, but not finding anything in our notes why - it may have occurred during the QC process. Guidance would be appreciated!

Link to this post | posted 10 May, 2018 19:14

rdejong

I have some students that wish to finish annotating genomes into the summer. The following question has come up for two students who have installed DNA Master on their own PC. They have been successful in getting DNA Master to update as well. The program is working except that in the Frames view, when the RBS data function is used, it only displays one set of measurements of RBS strength ('Shine Delgarno score and SD space'. The options to choose Z scores and Kibbler scores and the like are not there. Why might they be missing (new version?) and is it possible to get them back? I hesitated to start this as a new topic but I did not find any answer to this issue within any of the other threads. Thank you!

Link to this post | posted 10 May, 2018 19:00
rdejong	Thanks Kristen! We'll give it a try!

Link to this post | posted 10 May, 2018 01:14

rdejong

This will hopefully be a silly, easy-to-answer question! We don't typically use DNA Master for Mac in our course, but we have some students who wish to continue unfinished annotations into the summer. They have downloaded and installed the Wine Bottle version posted by Baylor (thanks SEA colleagues!), and it appears to run fine. However, some run into trouble in that they cannot open files - they just hang. My suspicion is that the files need to be in the DNA Master archives folder, only those files aren't 'seen' when in the Mac Finder. Is my suspicion correct or is something else? Any solutions? Thanks!

Link to this post | posted 20 Feb, 2018 20:10
rdejong	I have the same question as Greg, regarding the need to make notes about HHPred findings if BLASTP gives a strong function ID.

Link to this post | posted 22 Jan, 2018 19:43
rdejong	Dan Russell, I am having a real issue with getting 2017 SEA VM working on our Windows 10 computers. Can you get me the 2016 SEA VM that is 32 bit? Cal Keen ckeen@calvin.edu