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Title

 

 

 

 

 

BatchGenAna: a batch platform for large-scale genomic analysis of mammalian small RNAs

 

Authors

 

Xiaomin Ying1, You Jung Kim2, Yiqing Mao3, Ming Liu4, Yanyan Hou1, Hua Li1, Xiaolei Wang3, Yalin Zhao1, Dongsheng Zhao3, Jignesh M. Patel2, Wuju Li1*

 

Affiliation

 

1Center of Computational Biology, Beijing Institute of Basic Medical Sciences, Beijing 100850, China; 2Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, MI 48109, USA; 3Beijing Institute of Health Administration and Medicine Information, Beijing 100850, China; 4Beijing Medical Library, Beijing 100039, China

 

Email

 

liwj@bmi.ac.cn

 

Article Type

 

Software

 

Date

 

received January 21, 2009; accepted March 06, 2009; published April 21, 2009

 

Abstract

An increasing number of small RNAs have been discovered in mammals. However, their primary transcripts and upstream regulatory networks remain largely to be determined. Genomic analysis of small RNAs facilitates identification of their primary transcripts, and hence contributes to researches of their upstream regulatory networks. We here report a batch platform, BatchGenAna, which is specifically designed for large-scale genomic analysis of mammalian small RNAs. It can map and annotate for as many as 1000 small RNAs or 10,000 genomic loci of small RNAs at a time. It provides genomic features including RefSeq genes, mRNAs, ESTs and repeat elements in tabular and graphical results. It also allows extracting flanking sequences of submitted queries, specified genomic regions and host transcripts, which facilitates subsequent analysis such as scanning transcription factor binding sites in upstream sequences and poly(A) signals in downstream sequences. Besides small RNA fields, BatchGenAna can also be applied to other research fields, e.g. in silico analysis of target genes of transcription factors.

 

Keywords

small RNA; genomic analysis; primary transcript

Availability

The platform is freely available at http://biosrv1.bmi.ac.cn/BatchGenAna

Citation

Ying et al. Bioinformation 3(8): 346-348 (2009)

Edited by

P. Kangueane

 

ISSN

0973-2063

 

Publisher

Biomedical Informatics

 

License

 

 

This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.