Nucleic Acids Research Advance Access originally published online on May 8, 2007
Nucleic Acids Research 2007 35(Web Server issue):W27-W32; doi:10.1093/nar/gkm325
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Nucleic Acids Research, 2007, Vol. 35, No. suppl_2 W27-W32
© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
Articles |
Berkeley Phylogenomics Group web servers: resources for structural phylogenomic analysis
Berkeley Phylogenomics Group, University of California, Berkeley
*To whom correspondence should be addressed. Tel: 510 642 9932; Fax: 510 666 3327; Email: kimmen{at}berkeley.edu
Received January 31, 2007. Revised April 10, 2007. Accepted April 17, 2007.
Phylogenomic analysis addresses the limitations of function prediction based on annotation transfer, and has been shown to enable the highest accuracy in prediction of protein molecular function. The Berkeley Phylogenomics Group provides a series of web servers for phylogenomic analysis: classification of sequences to pre-computed families and subfamilies using the PhyloFacts Phylogenomic Encyclopedia, FlowerPower clustering of proteins sharing the same domain architecture, MUSCLE multiple sequence alignment, SATCHMO simultaneous alignment and tree construction and SCI-PHY subfamily identification. The PhyloBuilder web server provides an integrated phylogenomic pipeline starting with a user-supplied protein sequence, proceeding to homolog identification, multiple alignment, phylogenetic tree construction, subfamily identification and structure prediction. The Berkeley Phylogenomics Group resources are available at http://phylogenomics.berkeley.edu.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  Q. H. Christensen and J. E. Cronan The Thermoplasma acidophilum LplA-LplB Complex Defines a New Class of Bipartite Lipoate-protein Ligases J. Biol. Chem., August 7, 2009; 284(32): 21317 - 21326. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 R. S. Datta, C. Meacham, B. Samad, C. Neyer, and K. Sjolander Berkeley PHOG: PhyloFacts orthology group prediction web server Nucleic Acids Res., July 1, 2009; 37(suppl_2): W84 - W89. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Sankararaman, B. Kolaczkowski, and K. Sjolander INTREPID: a web server for prediction of functionally important residues by evolutionary analysis Nucleic Acids Res., July 1, 2009; 37(suppl_2): W390 - W395. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Dereeper, V. Guignon, G. Blanc, S. Audic, S. Buffet, F. Chevenet, J.-F. Dufayard, S. Guindon, V. Lefort, M. Lescot, et al. Phylogeny.fr: robust phylogenetic analysis for the non-specialist Nucleic Acids Res., July 1, 2008; 36(suppl_2): W465 - W469. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Wanchana, S. Thongjuea, V. J. Ulat, M. Anacleto, R. Mauleon, M. Conte, M. Rouard, M. Ruiz, N. Krishnamurthy, K. Sjolander, et al. The Generation Challenge Programme comparative plant stress-responsive gene catalogue Nucleic Acids Res., January 11, 2008; 36(suppl_1): D943 - D946. [Abstract] [Full Text] [PDF]
|
|