Skip Navigation

Nucleic Acids Research 2005 33(Database Issue):D495-D497; doi:10.1093/nar/gki090
This Article
Right arrow Full Text Freely available
Right arrow Print PDF (59K) Freely available
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Roth, C.
Right arrow Articles by Liberles, D. A.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Roth, C.
Right arrow Articles by Liberles, D. A.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Nucleic Acids Research, 2005, Vol. 33, Database issue D495-D497
© 2005, the authors
Nucleic Acids Research, Vol. 33, Database issue © Oxford University Press 2005; all rights reserved

The Adaptive Evolution Database (TAED): a phylogeny based tool for comparative genomics

Christian Roth, Matthew J. Betts, Pär Steffansson, Gisle Sælensminde and David A. Liberles*

Computational Biology Unit, BCCS, University of Bergen, 5020 Bergen, Norway

* To whom correspondence should be addressed. Tel: +47 55584043; Fax: +47 55584295; Email: liberles{at}cbu.uib.no

Received August 14, 2004; Revised and Accepted October 12, 2004

From 138 662 embryophyte (higher plant) and 348 142 chordate genes, 4216 embryophyte and 15 452 chordate gene families were generated. For each of these gene families, multiple sequence alignments, phylogenetic trees, ratios of non-synonymous to synonymous nucleotide substitution rates (Ka/Ks), mappings from gene trees to the NCBI taxonomy and structural links to solved three-dimensional protein structures in the Protein Data Bank (PDB) with Grantham-weighted mutational factors were all calculated. Of the ‘gene family trees’, 173 embryophyte and 505 chordate branches show Ka/Ks >> 1 and are candidates for functional adaptation. The calculated information is available both as a gene family database and as a phylogenetically indexed resource, called ‘The Adaptive Evolution Database’ (TAED), available at http://www.bioinfo.no/tools/TAED.

The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use permissions, please contact journals.permissions{at}oupjournals.org.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 J. Biol. Chem.Home page
M. Giannakis, H. K. Backhed, S. L. Chen, J. J. Faith, M. Wu, J. L. Guruge, L. Engstrand, and J. I. Gordon
Response of Gastric Epithelial Progenitors to Helicobacter pylori Isolates Obtained from Swedish Patients with Chronic Atrophic Gastritis
J. Biol. Chem., October 30, 2009; 284(44): 30383 - 30394.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
E. Proux, R. A. Studer, S. Moretti, and M. Robinson-Rechavi
Selectome: a database of positive selection
Nucleic Acids Res., January 1, 2009; 37(suppl_1): D404 - D407.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
Y. Tian and A. W. Dickerman
GeneTrees: a phylogenomics resource for prokaryotes
Nucleic Acids Res., January 12, 2007; 35(suppl_1): D328 - D331.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
C. R. Johnston, C. O'Dushlaine, D. A. Fitzpatrick, R. J. Edwards, and D. C. Shields
Evaluation of Whether Accelerated Protein Evolution in Chordates Has Occurred before, after, or Simultaneously with Gene Duplication
Mol. Biol. Evol., January 1, 2007; 24(1): 315 - 323.
[Abstract] [Full Text] [PDF]

Home page
 J. Bacteriol.Home page
H. Ichihara, K.-i. Kuma, and H. Toh
Positive Selection in the ComC-ComD System of Streptococcal Species.
J. Bacteriol., September 1, 2006; 188(17): 6429 - 6434.
[Abstract] [Full Text] [PDF]

Home page
 Plant Cell PhysiolHome page
S. Bhushan, A. Stahl, S. Nilsson, B. Lefebvre, M. Seki, C. Roth, D. McWilliam, S. J. Wright, D. A. Liberles, K. Shinozaki, et al.
Catalysis, Subcellular Localization, Expression and Evolution of the Targeting Peptides Degrading Protease, AtPreP2
Plant Cell Physiol., June 1, 2005; 46(6): 985 - 996.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.