CoMIC – Coevolution via MI on CUDA
The CoMIC (Coevolution via MI on CUDA) project tries to identify parts in a multiple sequence alignment (i.e. a set of DNA or protein sequences) that evolved in a coordinated way.
This website provides code as well as documentation for the CoMIC project.
For a given multiple sequence alignment we compute a so-called mutual information (MI) matrix (as shown in the image). High MI values for specific sequence positions may hint towards structural connections at the corresponding positions in the folded protein.
The picture illustrates the structure-coevolution signal: On the left we show a cluster of coevolving amino acids – indicated by high MI values – and on the right the corresponding secondary structures element; here the beta-sheet of the HIV1-protease.
If you want to get in contact regarding the project, please write to Kay Hamacher.
|The project is described in the following paper:|
CoMIC Version 1.2
The CoMIC code as well as the documentation may be used under the terms of the GPLv3 license of which you can obtain a copy here.
|1.2||Nov. 16, 2012||Code compiles on CUDA 5.0 and 4.x|
|1.1||Aug. 23, 2012||Reduced CPU RAM and GPU global memory usage to approximately one half for 2-point and one sixth for 3-point computations|
|1.0||Apr. 17, 2012||Initial Release. Computation of 2-point and 3-point MI, E(MI), E(MI^2) and percentiles|