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Recent Activity
All posts created by delesall
| Link to this post | posted 30 May, 2017 22:45 | |
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OK - I only see 4 databases as well. We have been selecting PDB and Pfam but not Scope. Since these are do novo annotation, I may add Scope95. However, the Scope database may disappear this summer per information on their web site (assuming I'm not confusing web sites) http://scop.berkeley.edu |
Posted in: Annotation → New HHPred web site
| Link to this post | posted 30 May, 2017 15:23 | |
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Hi Chris What databases do you pick to run a search? The menu of databases is much smaller, right? |
Posted in: Annotation → New HHPred web site
| Link to this post | posted 25 May, 2017 19:38 | |
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If you are annotating a podo virus, T7-like, do you go with terminase or with DNA packaging (traditionally used for T7-like pages, right?). Or are both equally OK? |
Posted in: Functional Annotation → Terminase vs DNA packaging
| Link to this post | posted 24 May, 2017 19:14 | |
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Hi all My students and I have been annotating a K1 phage and we have found some interesting HHPred matches. We are wondering whether these are sufficient to call funtion: Genes 39 and 40 - Both proteins show matches to ESAT6 family proteins - the first over only 20-25% of the aa sequence, the second over the whole aa sequence. Call function Virulence protein or NKF? Genes 94 and 95 - Nice HHPred matches - over 99%, whole length of aa sequence, very low E values -to HicB antitoxin and HicAtoxin - Call function? |
Posted in: Functional Annotation → K1 function call
| Link to this post | posted 24 May, 2017 18:43 | |
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Has anybody tried to use the new HHPred web site? I'm curious about which database we should select to run query? |
Posted in: Annotation → New HHPred web site
| Link to this post | posted 24 May, 2016 20:02 | |
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I do hope his family will take some small comfort in how widely David was loved and respected. Not many people can have the wide and positive impact David had, he will be missed but he will also be remembered. |
Posted in: Messages for Cabrini College → Messages for Cabrini College
| Link to this post | posted 08 Feb, 2016 01:22 | |
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I'm using HHPred tonight (Feb 7th) and can only see the databases pbd70_ and pfam_. There is no tigrfam_! Anybody knows what happened to that database? Thx, Veronique |
Posted in: Functional Annotation → HHPred databases
| Link to this post | posted 25 Sep, 2015 16:01 | |
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We have a student who cannot copy and paste into or within DNA Master. She can copy and paste outside of DNA Master on her computer and if she opens her DNA Master file on a different computer, she can copy and paste into and within DNA Master. Does she need to re-install DNA Master on her computer or is there a preference setting she needs to change? Any insights appreciated! Véronique |
Posted in: DNA Master → Copy and paste in DNA Master