Fungal Secretome Database: Integrated platform for annotation of fungal secretomes

Jaeyoung Choi; Jongsun Park; Donghan Kim; Kyongyong Jung; Seogchan Kang; Yong Hwan Lee

doi:10.1186/1471-2164-11-105

Fungal Secretome Database: Integrated platform for annotation of fungal secretomes

Jaeyoung Choi, Jongsun Park, Donghan Kim, Kyongyong Jung, Seogchan Kang, Yong Hwan Lee

Research output: Contribution to journal › Article › peer-review

153 Scopus citations

Abstract

Background: Fungi secrete various proteins that have diverse functions. Prediction of secretory proteins using only one program is unsatisfactory. To enhance prediction accuracy, we constructed Fungal Secretome Database (FSD).Description: A three-layer hierarchical identification rule based on nine prediction programs was used to identify putative secretory proteins in 158 fungal/oomycete genomes (208,883 proteins, 15.21% of the total proteome). The presence of putative effectors containing known host targeting signals such as RXLX [EDQ] and RXLR was investigated, presenting the degree of bias along with the species. The FSD's user-friendly interface provides summaries of prediction results and diverse web-based analysis functions through Favorite, a personalized repository.Conclusions: The FSD can serve as an integrated platform supporting researches on secretory proteins in the fungal kingdom. All data and functions described in this study can be accessed on the FSD web site at http://fsd.snu.ac.kr/.

Original language	English (US)
Article number	105
Journal	BMC genomics
Volume	11
Issue number	1
DOIs	https://doi.org/10.1186/1471-2164-11-105
State	Published - May 16 2010

All Science Journal Classification (ASJC) codes

Biotechnology
Genetics

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10.1186/1471-2164-11-105

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title = "Fungal Secretome Database: Integrated platform for annotation of fungal secretomes",

abstract = "Background: Fungi secrete various proteins that have diverse functions. Prediction of secretory proteins using only one program is unsatisfactory. To enhance prediction accuracy, we constructed Fungal Secretome Database (FSD).Description: A three-layer hierarchical identification rule based on nine prediction programs was used to identify putative secretory proteins in 158 fungal/oomycete genomes (208,883 proteins, 15.21% of the total proteome). The presence of putative effectors containing known host targeting signals such as RXLX [EDQ] and RXLR was investigated, presenting the degree of bias along with the species. The FSD's user-friendly interface provides summaries of prediction results and diverse web-based analysis functions through Favorite, a personalized repository.Conclusions: The FSD can serve as an integrated platform supporting researches on secretory proteins in the fungal kingdom. All data and functions described in this study can be accessed on the FSD web site at http://fsd.snu.ac.kr/.",

author = "Jaeyoung Choi and Jongsun Park and Donghan Kim and Kyongyong Jung and Seogchan Kang and Lee, {Yong Hwan}",

note = "Funding Information: This work was supported by the National Research Foundation of Korea grants (2009-0063340 and 2009-0080161) and grants from the Biogreen21 (20080401-034-044-009-01-00), the TDPAF (309015-04-SB020), and the Crop Functional Genomics Center (2009K001198). JC is grateful for the graduate fellowship through the Brain Korea 21 Program.",

year = "2010",

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doi = "10.1186/1471-2164-11-105",

language = "English (US)",

volume = "11",

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T1 - Fungal Secretome Database

T2 - Integrated platform for annotation of fungal secretomes

AU - Choi, Jaeyoung

AU - Park, Jongsun

AU - Kim, Donghan

AU - Jung, Kyongyong

AU - Kang, Seogchan

AU - Lee, Yong Hwan

N1 - Funding Information: This work was supported by the National Research Foundation of Korea grants (2009-0063340 and 2009-0080161) and grants from the Biogreen21 (20080401-034-044-009-01-00), the TDPAF (309015-04-SB020), and the Crop Functional Genomics Center (2009K001198). JC is grateful for the graduate fellowship through the Brain Korea 21 Program.

PY - 2010/5/16

Y1 - 2010/5/16

N2 - Background: Fungi secrete various proteins that have diverse functions. Prediction of secretory proteins using only one program is unsatisfactory. To enhance prediction accuracy, we constructed Fungal Secretome Database (FSD).Description: A three-layer hierarchical identification rule based on nine prediction programs was used to identify putative secretory proteins in 158 fungal/oomycete genomes (208,883 proteins, 15.21% of the total proteome). The presence of putative effectors containing known host targeting signals such as RXLX [EDQ] and RXLR was investigated, presenting the degree of bias along with the species. The FSD's user-friendly interface provides summaries of prediction results and diverse web-based analysis functions through Favorite, a personalized repository.Conclusions: The FSD can serve as an integrated platform supporting researches on secretory proteins in the fungal kingdom. All data and functions described in this study can be accessed on the FSD web site at http://fsd.snu.ac.kr/.

AB - Background: Fungi secrete various proteins that have diverse functions. Prediction of secretory proteins using only one program is unsatisfactory. To enhance prediction accuracy, we constructed Fungal Secretome Database (FSD).Description: A three-layer hierarchical identification rule based on nine prediction programs was used to identify putative secretory proteins in 158 fungal/oomycete genomes (208,883 proteins, 15.21% of the total proteome). The presence of putative effectors containing known host targeting signals such as RXLX [EDQ] and RXLR was investigated, presenting the degree of bias along with the species. The FSD's user-friendly interface provides summaries of prediction results and diverse web-based analysis functions through Favorite, a personalized repository.Conclusions: The FSD can serve as an integrated platform supporting researches on secretory proteins in the fungal kingdom. All data and functions described in this study can be accessed on the FSD web site at http://fsd.snu.ac.kr/.

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Fungal Secretome Database: Integrated platform for annotation of fungal secretomes

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