Link to this post | posted 11 Mar, 2021 18:07
GregFrederick@letu.edu	Awesome. Thanks for that Jackie. One more Q: How close do inverted repeats need to be in order to consider the sequence a "functional transposon"?

Link to this post | posted 10 Mar, 2021 19:31

GregFrederick@letu.edu

washj HI Welkin, The insertion element is identical to IS1096 which is present in smegmatis~ 16 copies (2278 bp in LouisV14 vs 2275bp in smeg - identical blast alignment e0.0; 3 bp diff may be due to sequencing error). The identification of IS10096 is detailed in the following paper from the Jacobs lab http://jb.asm.org/content/173/24/7772.full.pdf I propose the following designations: tnpA transposase tnpR resolvase Jackie Jackie- How did you locate the inverted repeats? We have a transposase hit stronger than that with Omega_21. I really want to call the gene. But identifying the actual presence of the transposon is something I am not 100% certain how to proceed at. Thanks for any insight you or others can provide. Greg

Link to this post | posted 10 Mar, 2021 19:20

GregFrederick@letu.edu

c.sunnen Okay! I'm QCing an F cluster (QuickMath) that calls a transposase. According to the approved functions list, there must be a tranposon. I don't know how to begin to check for this. Thanks! Great question. We are currently looking at a Cluster F (specifically F1) phage that has multiple 100% probability hits in NCBI blasts with other transposase. We are trying to look for inverted repeats surrounding the gene. But we do not see any other info the bioinformatics guide on how to identify an actual transposon in phage genomes. Is there a case study available on this. Our hit is much stronger than the reference phage gene in Omega_21. Any thought and or redirection to a case study on identifying transposons would be awesomeness! Thanks. Greg

Link to this post | posted 09 Feb, 2021 12:38

GregFrederick@letu.edu

Thanks Debbie. It has worked for some of our genomes this semester, with the previous settings. But the others start and then just sit there, even if left running for 24-36hrs. Thanks for troubleshooting. We will try to modified tRNA-Scan-SE settings. QUESTION: If the previous settings do run on a given genome, should we use the results obtained with those settings? Or should we rerun the analysis with the currently published settings? Thanks again for all your support! Greg

Link to this post | posted 09 Feb, 2021 12:38

GregFrederick@letu.edu

Thanks Debbie. It has worked for some of our genomes this semester, with the previous settings. But the others start and then just sit there, even if left running for 24-36hrs. Thanks for troubleshooting. We will try to modified tRNA-Scan-SE settings. QUESTION: If the previous settings do run on a given genome, should we use the results obtained with those settings? Or should we rerun the analysis with the currently published settings? Thanks again for all your support! Greg

Link to this post | posted 04 Feb, 2021 14:58

GregFrederick@letu.edu

It seems that the tRNA-Scan server listed in the Bioinformatics guide is currently broken. (http://trna.ucsc.edu/tRNAscan-SE/) We have been trying for several days to run the program on our four genomes and they all start and then the screen freezes and even if left overnight, they never finish. I can run the script above, but I would like for the students to be able to complete this exercise and have their personally generated files. Is there another tRNA-Scan-SE server available that I can direct them too? Other options they can use. Obviously, tRNA analysis can wait until later. But we have already introduced the concepts and students like to check boxes once they have have completed a task. Thanks. Greg

Link to this post | posted 25 Jan, 2021 20:57

GregFrederick@letu.edu

Is anyone else having difficulty getting Blast to run within DNA Master? It's not apparently working on my Office computer where it always has. (Yes. I ran the update and then restarted the program - multiple times.) It's not working on my Notebook computer. It is a fresh install there… Unlock is still "Hatfull" and no password, right? That's what is in the file on the setup link. DNA Master acts like is going through the Blast process. It gets to 100%. But even after 12-24 hours, if never writes the file and finishes the process. Anyone? Thanks. GF

Link to this post | posted 25 Jan, 2021 20:57

GregFrederick@letu.edu

Is anyone else having difficulty getting Blast to run within DNA Master? It's not apparently working on my Office computer where it always has. (Yes. I ran the update and then restarted the program - multiple times.) It's not working on my Notebook computer. It is a fresh install there… Unlock is still "Hatfull" and no password, right? That's what is in the file on the setup link. DNA Master acts like is going through the Blast process. It gets to 100%. But even after 12-24 hours, if never writes the file and finishes the process. Anyone? Thanks. GF

Link to this post | posted 02 Jun, 2020 22:08
GregFrederick@letu.edu	No problem. Hopefully this will keep someone else from banging their head! ha! gf

Link to this post | posted 02 Jun, 2020 22:07
GregFrederick@letu.edu	No problem. Hopefully this will keep someone else from banging their head! ha! gf