A. N. Nguyen Ba, B. J. Yeh, D. van Dyk, A. R. Davidson, B. J. Andrews, E. L. Weiss, A. M. Moses, Proteome-wide discovery of evolutionary conserved sequences in disordered regions. Sci. Signal. (2012) 5, rs1.
Its PubMed entry can be found here.
** New data from YGOB will soon be incorporated. **
The data and softwares for:
A. N. Nguyen Ba, B. Strome, J. J. Hua, J. Desmond, I. Gagnon-Arsenault, E. L. Weiss, C. R. Landry, A. M. Moses,
Detecting functional divergence after gene duplication through evolutionary changes in posttranslational regulatory sequences. PLoS. Comp. Biol. (2014)
can also be found in the data page.
Click here for the help page.
Click here to go back to the result page.
This file contains all predicted motifs in S.cerevisiae after filtering.
Cluster 1
This file contains all predicted clusters in the first cluster metric.
Cluster 2
This file contains all predicted clusters in the second cluster metric.
Cluster 3
This file contains all predicted clusters in the third cluster metric.
Software standalone
This file contains a tarball that includes v.1.0 of the phylo-HMM and instructions for usage. (Updated: A recent bug in the released version was fixed involving prediction of domains.)
Please read the README (Updated 4th of October of 2012) for proper data formatting as the software makes no effort into warning the user for improper usage. Further, note that the analysis performed by the phylo-HMM in this software package is incomplete and must be supplemented with appropriate additional filters.
Human motif file
This file contains motifs from the Ensembl data for human proteins using the second version of the phylo-HMM (see below).
This file contains a tarball that includes v.2.0 of the phylo-HMM and instructions for usage.
Please read the README and note that this version requires the acml or mkl C library for compilation. We recommend using this version from now on. See the manuscript or the help page for additional details on the changes incorporated in this version.
Simulation of protein evolution software
This file contains a tarball that includes v.1.0 of the software used to simulate protein evolution and instructions for usage.
Motifs with functional divergence
This table includes the motifs predicted in our second manuscript and whether they are likely to be functionally divergent after the whole-genome duplication.
Alignments used to detect functional divergence
This file contains a tarball that includes all the yeast alignments that were used to detect functional divergence in motifs.