title: sRNAMap: genomic maps for small non-coding RNAs, their regulators and their targets in microbial genomes.
abstract: 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/.
authors.affiliation: Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsin-Chu 300, Taiwan.
authors.forename: Hsi-Yuan
authors.initials: HY
authors.lastname: Huang
authors.forename: Heng-Yi
authors.initials: HY
authors.lastname: Chang
authors.forename: Chih-Hung
authors.initials: CH
authors.lastname: Chou
authors.forename: Ching-Ping
authors.initials: CP
authors.lastname: Tseng
authors.forename: Shinn-Ying
authors.initials: SY
authors.lastname: Ho
authors.forename: Chi-Dung
authors.initials: CD
authors.lastname: Yang
authors.forename: Yih-Wei
authors.initials: YW
authors.lastname: Ju
authors.forename: Hsien-Da
authors.initials: HD
authors.lastname: Huang
mesh_terms: D002874:Chromosome Mapping; D030561:Databases, Nucleic Acid / Q000706:statistics & numerical data; D015964:Gene Expression Regulation, Bacterial; D016680:Genome, Bacterial; D012329:RNA, Bacterial / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism*; D022661:RNA, Untranslated / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism*; D014584:User-Computer Interface
chemical_list: D012329:RNA, Bacterial; D022661:RNA, Untranslated