Link to this post | posted 01 Feb, 2016 04:04
lhughes	Have another one. Bubbles123 crashes on Pham 68 of 104. Lee

Link to this post | posted 01 Feb, 2016 03:29
lhughes	Lee Hughes Pham 38 or 71. Should be 38 OF 71

Link to this post | posted 01 Feb, 2016 02:42
lhughes	Chris - having trouble with Picard_Draft. It crashes on Pham 38 or 71. I cleared intermediate files and it still crashed. Lee

Link to this post | posted 29 Jan, 2016 20:01

lhughes

joyous726 We have something strange going on when we compare our auto-annotated Blast file in DNA master to what's in phamerator and starterator for ShiaLaBeouf_Draft. The gene product numbers/features don't align like they do for other phage genomes. It is probably because the auto-annotations came up with different results (yours compared to the one done for the phamerator file). Each time an auto-annotation is run there is a potential for a different result (just one additional gene call or non-call can throw off all the numbers). That is one of the reasons you always want your students to refer to genes by coordinates and not by gp#.

Link to this post | posted 27 Jan, 2016 17:12

lhughes

GregFrederick@letu.edu One more question: (OK. More than one!) We are having our students BlASTp the gene products that would be produced from all potential start codons, including the longest ORF, genemark, and glimmer calls and any other potential start codons in between. We just use the BLAST data that comes up from the NCBI blast in DNA Master as our starting point. If we have good data on the start (including Starterator) and the Q:T lineup is good, we don't look any further. I will only start doing BLASTs on other potential products if some of the other data doesn't support the call and I want to try other potential starts that could be better choices.

Link to this post | posted 27 Jan, 2016 04:42
lhughes	Another note about the difference between the data you get between PhagesDB blast hits and NCBI blast hits, even when the results are the same hits – on PhagesDB,you can sometimes get function information on hits where NCBI just says "gp12" and doesn't show you the function assignment.

Link to this post | posted 27 Jan, 2016 02:50
lhughes	I just ignore the updates personally. I might change to the new version after a semester, but never during. Don't want to take any chances that things will get mucked up.

Link to this post | posted 27 Jan, 2016 02:47

lhughes

Common mistake - they need to "post" data in a field before saving. When you start editing a feature, the symbol next to the row will change from an "arrow" to a "I" (indicates edits are happening). If you make changes and then immediately hit save while the "I" is still there, then the edits are not actually in the document information yet and will not be saved. There are two ways to "post". The simplest is to complete your edits, and then click on another row in the feature table. This automatically posts the information. The second is to hit the "post" button at the bottom of the table. Either posts the data to the program. Once this is done, when you hit "save" the changes will remain.

Link to this post | posted 27 Jan, 2016 02:42
lhughes	"FS:" stands for Function Source. This is the source of the data you provided in "F:" (so NCBI Blast, or PhagesDB Blast, HHPRED, etc.)

Link to this post | posted 26 Jan, 2016 04:59
lhughes	I installed DNA Master on my new laptop that runs Windows 10 and don't remember having any problems getting it up and running. Lee