Protein function prediction using the Protein Link EXplorer (PLEX).
We introduce the Protein Link EXplorer (PLEX), a web-based environment that allows the construction of a phylogenetic profile for any given amino acid sequence, and its comparison with profiles of approximately 350,000 predicted genes from 89 genomes, as a means of interactively identifying functionally linked genes and predicting protein function. PLEX can be searched iteratively and also enables searches for chromosomal gene neighbors and Rosetta Stone linkages. PLEX search results are accompanied by quantitative estimates of linkage confidence, enabling users to take advantage of coinheritance, operon and gene fusion-based methods for inferring gene function and reconstructing cellular systems and pathways.


BACKGROUND
http://bioinformatics.icmb.utexas.edu/plex
Date
Shailesh V
SV
Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, 1 University Station, A4800, Austin, TX 78712-1064, USA.
Marcotte
Edward M
EM
D000465:Algorithms; D000595:Amino Acid Sequence; D003196:Computer Graphics; D019143:Evolution, Molecular; D008969:Molecular Sequence Data; D010802:Phylogeny; D011487:Protein Conformation; D011506:Proteins / Q000032:analysis* / Q000737:chemistry / Q000378:metabolism*; D016415:Sequence Alignment / Q000379:methods; D020539:Sequence Analysis, Protein / Q000379:methods*; D017386:Sequence Homology, Amino Acid; D012984:Software; D013329:Structure-Activity Relationship; D014584:User-Computer Interface
D011506:Proteins