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Bioinformatics Advance Access published online on February 26, 2008
Bioinformatics, doi:10.1093/bioinformatics/btn058
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© 2008 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.

FTFD: An Informatics Pipeline Supporting Phylogenomic Analysis of Fungal Transcription Factors

Jongsun Park 1,2,3, Jaejin Park 1,2, Suwang Jang 1, Seryun Kim 1,2, Sunghyung Kong 1,2, Jaeyoung Choi 1,2, Kyohun Ahn 1, Juhyeon Kim 1, Seungmin Lee 1, Sunggon Kim 1, Bongsoo Park 5, Kyongyong Jung 1,2, Soonok Kim 3,4, Seogchan Kang 5 and Yong-Hwan Lee 1,2,3,4,*

1Fungal Bioinformatics Laboratory, 2Department of Agricultural Biotechnology, 3Center for Fungal Genetic Resource, 4Center for Agricultural Biomaterials, Seoul National University, Seoul 151-921, Korea and 5Pennylvenia State University, University Park, PA 16802, USA

*To whom correspondence should be addressed. Prof. Yong-Hwan Lee, E-mail: yonglee{at}snu.ac.k


  Abstract

Summary: Genomes of more than 60 fungal species have been sequenced to date, yet there has been no systematic approach to analyze fungal transcription factors (TFs) kingdom-widely. We developed a standardized pipeline for annotating TFs in fungal genomes. Resulting data have been archived in a new database termed the Fungal Transcription Factor Database (FTFD). In FTFD, 31,832 putative fungal TFs, identified from 62 fungal and 3 Oomycete species, were classified into 61 families and phylogenetically analyzed. The FTFD will serve as a community resource supporting comparative analyses of the distribution and domain structure of TFs within and across species.

Availability: All data described in this study can be browsed through the FTFD web site at http://ftfd.snu.ac.kr/.

Contact: yonglee{at}snu.ac.k

Associate Editor: Dr. Jonathan Wren

Received on November 18, 2007; revised on January 17, 2008; accepted on February 10, 2008

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