User: michael

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michael0
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Posts by michael

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Protein-Protein interaction modelling without 3D structure
... Hi, I am currently looking into four proteins that are supposed to interact with each other. I would like to find out what exact residues are responsible for the interaction, the only problem is that I don't have a structure for any of them. All of the algorithms I've found require a known structur ...
protein-protein-interaction modelling written 7 months ago by michael0 • updated 6 months ago by Biostar ♦♦ 20
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Comment: C: Strategies for identifying as many homologs as possible
... Hi Michael, thanks so much for your detailed answer! I agree that I do not need to be too worried about missing a few orthologs here and there. That being said, I would like to have a table stating how many species within different subgroups have a copy of this gene (e.g. 28 Fungi have a homolog). ...
written 13 months ago by michael0
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Strategies for identifying as many homologs as possible
... I am working on a follow-up to a study done in 2006. In it, the authors attempted to identify "all homologs" of a gene (using blastp and tblastn) and they looked at its likely evolution. (The gene is very highly conserved across species). There were a number of interesting questions that the authors ...
homology phylogenetics est msa blast written 13 months ago by michael0 • updated 13 months ago by Michael Dondrup46k
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Neighbor Joining algorithm: why n-2?
... I have been looking into how the neighbor joining algorithm works and I have two questions about the first step, i.e. computing the matrix Q using the following formula: > Q(i,j) = (n - 2)d(i,j) - Σd(i,k) - Σd(j,k) Where both summations are from k = 1 to n, n is the number of taxons, d() is the ...
neighbor-joining phylogenetics evolution written 18 months ago by michael0 • updated 18 months ago by kloetzl1.0k

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