Hot answers tagged structure-prediction
I looked for relevant publications at Web of Science using 'structur* AND cyclodextrin' in the Title field. For the period 2011-2012 there were 56 hits including: Racz et al (2012) Structure of the inclusion complex of beta-cyclodextrin with lipoic acid from laboratory powder diffraction data. Acta Crystallographica Section B 68: 164-170 Ali et al ...
Have you used hhpred to search for homologues? What was your criteria for defining there was no homologues? You could potentially go down to around 30% sequence identity to model. I would submit the the query sequence to both I-Tasser and Rosetta and see if both of the servers agree on the topology. I-Tasser will always provide 5 models of your query ...
Robetta's the best service I've found for a protein I'm working on that doesn't have a solved structure. It's down right now for the CASP10 competition, but I would submit it and wait. The wait time lately has been ~2 months.
You can use R-coffee of the T-coffee suite of tools. In general, the *coffee tools are excellent and work very well if you can get over their author's self obsession1. R-coffee can align RNA sequences taking into account structural information: 1 The guy actually adds his name to the output of all his programs! Seriously, he does. Apart from being ...
I frankly don't trust Mfold or RNAfold for finding structure. There are just too many false positives and without experimental verification, it's not reliable. For finding hypothetical local structure, it's great. However to find evolutionary conserved structure MSA methods like what has been used with Rfam are a more suitable way. Since you asked for ...
there a number of tools in the Vienna package (RNAalifold, RNALalifold): http://www.tbi.univie.ac.at/~ronny/RNA/index.html some other tools are available from Freiburg Univ. such as: LocARNA or CARNA (http://rna.informatik.uni-freiburg.de/CARNA/Input.jsp)
There is no hard and fast rule for how many nucleotides you have to select. If your miRNA is ~20nt and you take 70nt from both sides (average length of hairpins is ~84nt in humans), your total length will be 160nt. The point of taking $\pm70nt$ is that you don't know if your read is -3p or -5p. So take 70nt from both sides. The maximum length of a human ...
There won't be any duplicates in miRBase (for a given organism). Choose the taxon nearest to your organism if you are doing homology based discovery. If you want to take all/many organisms then you can use fastx_collapser to collapse redundant sequences. However you will lose the name of the miRNA. You can use awk also for this and it will keep the sequence ...
The green region will definitely not make an miRNA: It is not a part of a stem loop. See typical miRNA structures from miRbase. EDIT Bulges can sometimes determine which strand is chosen as mature miRNA. However, this green region is also is unlikely to form miRNA because the stem is just 15bp.
I think your suggestions are fine - there are a few ways you could write this. I might use some variant of; The techniques used may be specific to the research question, and particular considerations may also be required depending on the accepted norms within the academic field
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