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All posts created by coomansr

| posted 05 Jan, 2017 18:53
coomansr avatar
coomansr
Two of the four phages we had sequenced in December, Aggie and Philonius, would not run on Starterator. Both are Cluster N, and both crashed on pham 21476, which was pham 52 of 70 in Aggie and pham 52 of 72 in Philonius. I am using the new SEA 2017 VM and the database is up to date. Any suggestions?
Posted in: Starterator → phage that crash starterator
| posted 03 Jan, 2017 14:29
coomansr avatar
coomansr
I've been unable to access the Lawrence Lab homepage to download DNA Master. I've tried repeatedly, with different browsers. Is the site down?
Roy
Posted in: DNA Master → Site down?
| posted 13 Apr, 2016 20:20
coomansr avatar
coomansr
Welkin,

Here's my top hit on HHpred. I'm thinking the answer is yes, but I'm not sure how to interpret HHpred results in detail.

>1zoi_A Esterase; alpha/beta hydrolase fold; 1.60A {Pseudomonas putida} SCOP: c.69.1.12 PDB: 4dgq _A
Probab=100.00 E-value=2.3e-38 Score=242.53 Aligned_cols=255 Identities=24% Similarity=0.255 Sum_probs=0.0
96Kb
Posted in: Functional Annotation → hydrolase, esterase or hydrolase/esterase?
| posted 12 Apr, 2016 22:13
coomansr avatar
coomansr
Which is the preferred function annotation?

TiroTheta9_59, hydrolase, 274 537 e-153
Sabertooth_60, esterase, 274 537 e-153
Melvin_MELVIN_62, hydrolase/esterase, 274 537 e-153
Posted in: Functional Annotation → hydrolase, esterase or hydrolase/esterase?
| posted 19 Feb, 2016 22:05
coomansr avatar
coomansr
Thanks for the file on Mazhar510, and for the quick turnaround. Roy
Posted in: Starterator → phage that crash starterator
| posted 17 Feb, 2016 23:12
coomansr avatar
coomansr
Thanks for the file on Roosevelt. I've tried running Mazhar510_Draft 3 times and each time it stops on pham 2 of 87, pham 16401. The other one I ran this week, Royals2015, worked without a hitch! Any help you can provide with Mazhar510 is appreciated. Roy
Posted in: Starterator → phage that crash starterator
| posted 16 Feb, 2016 21:11
coomansr avatar
coomansr
All,
We have the same. Do you suggest just using the other 2 databases or selecting another as a third?
Roy
Posted in: Functional Annotation → HHPred databases
| posted 03 Feb, 2016 22:34
coomansr avatar
coomansr
Roosevelt_Draft won't run. After numerous attempts I followed the "Read This" suggestions and cleaned out the Intermediate Files folder. Still crashed on pham 21 of 89, pham 5238. Typically it crashes on pham 39. Once or twice it has made it past that one, but it's never run to completion.

Roy
Edited 03 Feb, 2016 22:36
Posted in: Starterator → phage that crash starterator