Link to this post | posted 13 Sep, 2016 20:55

debbie

Hi all, Attached is a list of participants of the Xeno Project. Check to see that you are included if you indeed signed up! The MTA process was begun at Pitt on Friday, Sept. 9, 2016. MTAs are currently under review in Pitt's Office of Research. Once they have passed that process, they will be coming to you and your legal contact person for signatures. Please sign and return immediately! If all goes well, we can ship in early October. If you are participating in the Host Range project, your MTA includes materials for both projects. I have updated the participant list today 9-29-16. Edited 29 Sep, 2016 16:21 19Kb

Link to this post | posted 06 Aug, 2016 12:11
debbie	Joe, HI! If you haven't lost volume (water), I think you are OK. If you have dropped the volume significantly, you might want to add some sterile water. I don't think you will have trouble with the degradation of small molecules. Just include its date in your lab notebook, so if a pattern presents itself, you will be able to link it to this component.

Link to this post | posted 22 Apr, 2016 19:17

debbie

This is difficult to answer without seeing the data. In general, you will want to choose the best start (just like any protein) for the G of the G/T tail assembly chaperone proteins. T will have the same start, so you need not repeat what you said for G. The function is Tail assembly chaperone. The source of that function info is most likely phagesDB (phamerator). I don't know what "logic" means in this context. you can add that it is a -1 frameshift in your notes. When you record your start justification 1:1 with Gideon is appropriate.

Link to this post | posted 22 Apr, 2016 18:22

debbie

Greg, I assume you are speaking of the Cluster A6 mycobacteriophage WonderPhul, gp6. I don't think it is the major tail protein. I believe that gp26, pham 19254 is the major tail protein. In addition, Cluster A6 phages are siphoviridae, and I don't believe they have a tail sheath. I am not sure what you are calling there. Mycobacteriophages can have many minor tail genes, so calling more than one if you have evidence is predictable. When I HHPred gp 6 (pham 17521), the best hits are to collagen. Phages won't have collagen, but this protein is aligning with collagen because of the GPX motif that is present. We are assuming that has to be a minor tail protein. Prudently, I would not assign a function. But as you can see others have.

Link to this post | posted 02 Mar, 2016 18:30

debbie

Keith, I asked Dr. Lawrence about this and here is his response: "Yes, DNA Master will wait until the BLAST server send replies; the delays are due to the failures of the BLAST server to return results in a timely fashion. Outside of abandoning searches and resubmitting the data - which they explicitly tell you not to do as it simply overloads the servers - there it nothing one can do. Their policy does ignore the possibility that the server may never return the results, or return them after an inordinate amount of time." Not very satisfying, but may help us to understand. I blasted a genome yesterday that produced the usual errors and took 8 hours to complete, but it did finish.

Link to this post | posted 29 Feb, 2016 23:43
debbie	Success! I blasted an entire phage genome (52KB) and finished the blast. The blast log details that the blast finished in about an hour, but it could not retrieve all of the blast data for about 3 additional hours. However, the blast did finish and it is looking good so far!

Link to this post | posted 29 Feb, 2016 19:34
debbie	Hi all! I was just able to blast a gene (and repeated by Dan) in DNA Master. The Integer Overflow error is gone and my posted wait time was 31 seconds, with the blast data returned in about 1 1/2 minutes. I just started to Blast an entire genome and will keep you posted as to how that goes! We are back in business!

Link to this post | posted 27 Feb, 2016 22:15
debbie	Hi all. It is not a DNA Master issue, but rather an NCBI Blast error. Note when you blast, it returns an error message "integer overflow" and tells you that the wait time is a couple of years (mine said 54956368 seconds). We have been in contact with NCBI and they "are working on it". in the meantime, you can blast one gene at a time and record your results. We will keep you posted.

Link to this post | posted 11 Feb, 2016 22:18
debbie	Greg, Though it is always helpful to know the whole context, I think you are asking about what GeneMark calls a possible frameshift. It has identified some sort of ribosomal slippage. Know that we do not call any frameshifts except for the programmed frameshift found in the tail assembly chaperones found upstream of the tape measure protein. Make sense?

Link to this post | posted 27 Jan, 2016 20:50

debbie

Tammy, The best answer is all of the above! I use GeneMarkS and GeneMark with Arthrobacter FB24. Whatever you use, record that in your cover sheet. The one directed at self is the same info as what comes in through the auto-annotation, just in picture form. So it is not additional info. Both GeneMark against self and against a host are helpful and informative. Blasting against phagesDB (and Phamerator - which is the same data) is just identifying what we already know. Now that we have >45 Arthrobacter phage genomes finalized and in GenBank, you should find more helpful info there. However, I will always say you should run an NCBI BLast because there is always new data being posted there. Likewise, HHPred should be run with the 3 databases pbd70_, pfamA_, and tigrfam_. Again new data is showing up there regularly and we are able to identify more functions to our genes than ever before.