Biostar Beta. Not for public use.
Question: Plotting Selection On Structures
1
Entering edit mode

Similar to Evolutionary Trace, it should be possible to plot levels of selection (omega or a related number) on existing structures. But all I can find is SWAKK, which only allows two sequences, hence works with a window. I really just want to plot omega values of residues, calculated based on a >10 sequences MSA, on a structure. Does this exist? I am not into programming but it seems no too difficult, hence if it doesn´t exist I might ask my students to do this but if it already exists...Cheers

ADD COMMENTlink 7.8 years ago Arjen Ten Have • 350 • updated 19 months ago Biostar 20
2
Entering edit mode

Have you looked at ConSurf server or ConSurfDB ?
Consurf uses Rate4Site to derive phylogenetic tree of the homologues using the neighbor joining algorithm (using the JTT substitution model).

enter image description here

ADD COMMENTlink 7.8 years ago Khader Shameer 18k
0
Entering edit mode

Hi Khader

Tx for you reply. Consurf is similar to Evolutionary Trace and shows variation at the amino acid level. Typically you need or at least use divergent datasets and you look at divergence (hence difference between species). What I want is for instance to determine which part of a protein is under positive selection. DNAsp can determine which stretches of sequences are under positive selection and yields basically a numerical output, this I want to plot on a PDB strcuture. For this type of analysis you use nucleotide sequences of strains or varieties, hence you are looking at polymorhisms (differences within spècies level) and you calculate the ratio of non-synonymous to synonymous mutations. Such that you have an idea: the sequences you use are typically 95-98% identical. Consurf cannot do anything with this. In reality right now I will be helped by simply plotting the data on a PDB, in the future I foresee I want to screen in 3D space but that is way more complicated!!

ADD COMMENTlink 7.8 years ago Arjen Ten Have • 350
Entering edit mode
0

AFAIK, Consurf works well with both nucleic acid sequence and amino acid sequences. The metric is similar to the approach you are mentioning (See the detailed methodology http://consurf.tau.ac.il/overview.html) but not exactly the same.

ADD REPLYlink 7.8 years ago
Khader Shameer
18k

Login before adding your answer.

Similar Posts
Loading Similar Posts
Powered by the version 2.0