Methods for detecting inter-protein covarying sites
| dc.contributor.author | Ackermann, Robert | en |
| dc.contributor.author | Zhang, Liqing | en |
| dc.contributor.department | Computer Science | en |
| dc.date.accessioned | 2013-06-19T14:35:47Z | en |
| dc.date.available | 2013-06-19T14:35:47Z | en |
| dc.date.issued | 2009 | en |
| dc.description.abstract | Covarying sites are defined to be sites in a protein whose rate of evolution changes over time. We design software to group protein sites into three rate pools: conserved, variant, and temporary invariant. Other software is written to find sites which are closely correlated. The algorithms used by the software require a multiple sequence alignment and phylogenetic tree as input and rely heavily on tree-corrected information entropy. Through a study of the protein Cu, Zn Superoxide Dimutase it is shown that temporary invariant sites have interactions with at least one site which is either closely correlated or binary-switching. From this result it is reasonable to assume that temporary invariant sites which interact with no such intra-protein sites must be sites of protein-protein interaction. Temporary invariant sites are also shows to reflect the animal plant divergence. | en |
| dc.format.mimetype | application/pdf | en |
| dc.identifier | http://eprints.cs.vt.edu/archive/00001080/ | en |
| dc.identifier.sourceurl | http://eprints.cs.vt.edu/archive/00001080/01/RobPaper.pdf | en |
| dc.identifier.trnumber | TR-09-22 | en |
| dc.identifier.uri | http://hdl.handle.net/10919/20106 | en |
| dc.language.iso | en | en |
| dc.publisher | Department of Computer Science, Virginia Polytechnic Institute & State University | en |
| dc.rights | In Copyright | en |
| dc.rights.uri | http://rightsstatements.org/vocab/InC/1.0/ | en |
| dc.subject | Software engineering | en |
| dc.title | Methods for detecting inter-protein covarying sites | en |
| dc.type | Technical report | en |
| dc.type.dcmitype | Text | en |
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