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All posts created by cmageeney

| posted 26 Oct, 2017 14:12
Hi Dan,

Thank you this did fix one of the problems.

We have a second problem as well. The student gets an error "Data module error" Then lists many databases. See Image.

Do you have any way to fix this problem? The student has tried to uninstall and reinstall without success. He tried to hard remove from the computer and a system restore point.

Posted in: DNA MasterSSL error
| posted 24 Oct, 2017 14:47

One of my students is getting the error "could not load SSL library". when he tried to BLAST.

Does any one know how to fix this bug?

Posted in: DNA MasterSSL error
| posted 12 Mar, 2017 16:01
Hi Lee,

I actually started all of this on Vassie's account. I know she has admin right. Since it did not work under her account, she created an admin account for me. I can add additional users and get into the admin setting so I assume I have admin privileges.

I'll send Claire an email.

Posted in: PECAANPhage can not be added
| posted 10 Mar, 2017 19:50

Lehigh is new to using PECAAN. I have tried quite a few times this week to use PECAAN with a streptomyces phage Warpy (BE1). I followed all the instructions in the most recent guide from Dec 7, 2016. The longest I have let the site run is 24 hours and the phage still has not been added to the database. Any ideas?
Katie Mageeney
Posted in: PECAANPhage can not be added
| posted 17 Jan, 2017 02:04
Thanks Chris!

After I wrote this I noticed that I was using an older phamerator file, I had a few more genes move to new phams. Once I updated the phamerator file, I solved my problem.

Posted in: StarteratorRead First: Common Starterator Troubleshooting
| posted 14 Jan, 2017 22:49
Hi Chris,

I am currently having issues with starterator in the virtual machine. I have been using the website you created to finish the starterator data that students missed for our phage Kevin1. I was looking through the list for pham 21227 and noticed it is not there. Is there any way I can access this in lieu of the virtual machine.

Katie Mageeney
Lehigh University
Posted in: StarteratorRead First: Common Starterator Troubleshooting
| posted 15 Dec, 2016 16:32
Hi Debbie,

We have tested all the phages that Lehigh has isolated on the Xeno lawn. How would you like the results delivered?

Katie Mageeney
Posted in: Xeno ProjectHow to Record Results
| posted 20 Oct, 2016 12:48
Hi All,

At Lehigh we will be using the strains Mycobacterium austroafricanum and Microbacterium natoriense.
Posted in: Host-Range ProjectBasic Host Range Project Information
| posted 13 Apr, 2016 18:00
Hi Dan,

I was wondering if I could be sent the link for the new virtual machine. My entire virtual box is not working and I trying to reinstal everything. I would need the windows version.


Katie Mageeney
Posted in: SEA-PHAGES Virtual MachineStudent download of 2016 VM
| posted 27 Jan, 2016 04:13

1. Are both blasts really necessary?
Both blast are important because they give you different data. The NCBI blast will give you all information while phagesdb blast will only give you actinobacter phages. You can however individually blast each gene product as you annotate in DNAmaster. I find this helpful for students since they can then make start site changes and re-blast, when necessary. What I typically do is set my personal file to blast overnight. I have never had a problem doing it that way then I have all the data needed.

2. What might the PhagesDB BLASTp turn up that the NCBI would not (archived phage genes, I suppose.)?
phagedb is going to show all the blast hits in actinobacter phages. This may be useful if you are looking for other phages that are not in genbank yet.

3. What might the NCBI BLASTp turn up that the PhagesDB BLASTp would not? So far, they are identical.
NCBI will turn up many additional results that phagesdb is not set for. These could be hits in bacterial species, other types of phages, such as coli phages.

4. HHPred returns completely different regional homologies. Is there a threshold, i.e. number of AAs in a string that might be of interest?
We ask our students to use their best judgement about functional information here. I use 95% homology and e-values higher than 10^-5. This is not a hard rule but a good guideline to start with.

5. In HHPred if the query sequence is 150aa long and a homologous stretch of 18-20aa is return in say an "E. coli DNA Gyrase Inhibitor" can/should we ignore such short homologies?
Take all information into consideration but use your best judgement.

Hope this helps and anyone else that has information to answer these that I might have missed feel free to jump in.
Posted in: DNA MasterPhagesDB vs NCBI BLASTp results - the value of both?