The Adaptive Evolution Database (TAED) 3.0
A NEW VERSION OF TAED IS CURRENTLY AVAILABLE AT http://www.bioinfo.no/tools/TAED.
This is a resource meant to detail known events that can be linked to adaptive evolution. So far, this database includes information on coding sequence evolution as assessed by Ka/Ks ratios recalculated from the Master Catalog grouping of all chordate nuclear genes found in Genbank (see this manuscript for information on methodology). In the future, building of in house families at closer PAM distance will allow better examination of orthologues and will allow us to display trees and multiple sequence alignments on this website (as was done in the original version).
As data becomes available, additional types of evolution will also be characterized in this database. If you have data that you wish to share in the context of this database, please send me an email at liberles@sbc.su.se.
It should be noted that only with completed genome sequences can statements about gene loss be made. This data will be added as complete genome sequences from chimpanzee, mouse, etc. arrive.
This information is derived from information in several other databases.
The Master Catalog is a genetic sequence database organized by evolutionary families. In the version used, every protein found in Genbank was grouped into a familiy of related sequences with associated multiple sequence alignments and phylogenetic trees.
EGAD is a TIGR database that links expression data, cellular roles and alternative splicing information in a curated, non-redundant set of human transcript sequences.
PMD provides information on what kind of functional and/or structural influences are brought about by amino acid mutation at specific positions of a protein including what phenotype a certain mutation gives rise to.
PDB provides structural information on proteins with known solved three dimensional structures. Homology models were built for each protein with a close homologue and Grantham-weighted mutations along the TAED branch were mapped onto the homology model using a new method (Almgren, M.A.E., 2001, M.Sc. thesis, Stockholm University).
You can search this database in three ways:
1. From a protein/biochemical point of view:
Here all proteins from chordates with branches containing Ka/Ks values greater than 0.6 utilizing the method of Liberles (Liberles, D.A. 2001. Molecular Biology and Evolution, in press.) are available to search.
The parenthesis next to the protein names indicates what information you can find.
2. From a phylogenetic point of view:
The chordate tree of life is presented (using NCBI taxonomy), where each branch is clickable to view the known molecular events that may be adaptive that are occurring at that point in evolutionary history.
3. From a metabolic point of view:
In each metabolic pathway or classification (based upon the EGAD database), points where specific proteins from TAED with sequence similarity appear to be undergoing adaptive evolution can be viewed.
A list of high Ka/Ks proteins is also available. The parenthesis next to the protein names indicates what information you can find.
TAED 2.1 is still accessible. Version 2.1 contains information from both chordates and embryophyta based on calculation using the PBLSB method for calculating Ka/Ks ratios and was calculated using the complete Master Catalog (see Benner, S.A., Trabesinger, N., and Schreiber, D. 1998. Adv. Enz. Reg. 38: 155-180).
More information about this database can be found at:
1. Benner, S.A., Chamberlin, S.G., Liberles, D.A., Govindarajan, S., Knecht, L. 2000. Research in Microbiology, 151:97-106.
2. Liberles, D.A., Schreiber, D.R., Govindarajan, S., Chamberlin, S.G., and Benner, S.A. 2001. Genome Biology, 2(8):research0028.1-0028.6.