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Nucleic Acids Research Advance Access originally published online on November 16, 2008
Nucleic Acids Research 2009 37(Database issue):D150-D154; doi:10.1093/nar/gkn852
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Nucleic Acids Research, 2009, Vol. 37, Database issue D150-D154
© 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.

This article appears in the following Nucleic Acids Research issue: Database issue [View the issue table of contents]

Articles

sRNAMap: genomic maps for small non-coding RNAs, their regulators and their targets in microbial genomes

Hsi-Yuan Huang1, Heng-Yi Chang1, Chih-Hung Chou2, Ching-Ping Tseng2,3, Shinn-Ying Ho1,3, Chi-Dung Yang3, Yih-Wei Ju3 and Hsien-Da Huang1,3,4,*

1Institute of Bioinformatics and Systems Biology, 2Institute of Molecular Medicine and Bioengineering, 3Department of Biological Science and Technology and 4Core Facility for Structural Bioinformatics, National Chiao Tung University, Hsin-Chu 300, Taiwan

*To whom correspondence should be addressed. Tel: +886 3 5712121 Ext. 56952; Fax: +886 3 5729288; Email: bryan{at}mail.nctu.edu.tw

Received August 20, 2008. Revised October 9, 2008. Accepted October 16, 2008.

Small non-coding RNAs (sRNAs) carry out a variety of biological functions and affect protein synthesis and protein activities in prokaryotes. Recently, numerous sRNAs and their targets were identified in Escherichia coli and in other bacteria. It is crucial to have a comprehensive resource concerning the annotation of small non-coding RNAs in microbial genomes. This work presents an integrated database, namely sRNAMap, to collect the sRNA genes, the transcriptional regulators of sRNAs and the sRNA target genes by integrating a variety of biological databases and by surveying literature. In this resource, we collected 397 sRNAs, 62 regulators/sRNAs and 60 sRNAs/targets in 70 microbial genomes. Additionally, more valuable information of the sRNAs, such as the secondary structure of sRNAs, the expressed conditions of sRNAs, the expression profiles of sRNAs, the transcriptional start sites of sRNAs and the cross-links to other biological databases, are provided for further investigation. Besides, various textual and graphical interfaces were designed and implemented to facilitate the data access in sRNAMap. sRNAMap is available at http://sRNAMap.mbc.nctu.edu.tw/.


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