Wednesday, August 22, 2007

Method for applying spectral biclustering algorithm

Regarding your spectral biclustering algorithm, I need to apply it for biclustering of web pages to analyse Internet users behaviour. Would you mind tell me what was the tool you used to apply this algorithm or send me the program if it's possible as I need to apply many biclustering algorithms and it's impossible for me to program all them.

The code was written in MATLAB. The key steps involve using an iterative bi-normalization procedure followed by the standard SVD function. The subsequent steps involve partitioning of the left and right eigenvectors using a k-means like procedure.

We have not put all the components in one fully automated version. If you think that getting the components is useful for you I will dig in the directories of my old computer.

Turning morph to a movie

I have a morph I created some time ago that illustrates an essential motion in the protein I study. I'd like to have the morph as part of my thesis talk. Can I turn it into a movie that I can store on my computer and have as a part of my power point presentation (in other words, can I have a copy of it so that I don't have to access the webpage?). How do I do this? Are there obvious directions on teh webpage that I"m just missing?

On the jmol morph page you will see a link that says:

Orient the molecule to your liking and then:
Generate high-res gif

Unfortunately it is just a wireframe animation. I had it set to do cartoons but for some reason it's back to wireframe now.

Alternatively, you can download the interpolated trajectory, then animate using vmd or jmol.

Look for an NMR-formatted PDB file called movie.pdb here:

Compiled Sequences for Human and Chimp

I am seeking sequences for all the pseudogenes listed in the flat files for (at minimum) human and chimp ( 9606.71.gtf and 9598.2.gtf). I tried to look at the assembled sets on the website but I only found compiled sequences for processed or putative pseudogenes, and not duplicate pseudogenes. I wanted to ask you if there are files somewhere on the site that have sequence data for all pseudogenes listed in the species gtf files.

Sorry, we don't have that.

Monday, August 20, 2007

Local Clustering of Expression Data Software Download

I am interested in using your local clustering of expression data software
(J Mol Biol. 2001 Dec 14;314(5):1053-66). I would really appreciate if
you provide me the link to download the software for my academic use.

Friday, August 17, 2007

Real motions for residues in paper "Normal Modes for Predicting Protein Motions"

About your paper "Normal Linkmodes for predicting protein motions". Probably, I miss something when I'm reading... I didn't understand how you get the real (observed) motions for residues? Did you perform MD simulation for all proteins in your set?

Regarding my "Normal modes" paper: the “real (observed) motions for residues” are not
actually “real motions” – as long as we could find two substantially different conformations for the same protein in PDB, we assumed that such motion (1st conformation and 2nd one) could potentially take place. We didn’t do any MD simulations in that paper (although, we did possess technologies that would allow us to simulate such motion – e.g. our MorphServer). In our normal modes paper we figured that any such simulation is unnecessary – all we needed for that study was just a set of vectors connecting the residues from the two conformations (to examine how they correlate with the NM-predicted motion vectors).