Aug 27, 2009

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

Bioinformation
Xiaomin YingWuju Li

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

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Mentioned in this Paper

Genome
Genomics
Expressed Sequence Tags
Transcription Factor
Flank (Surface Region)
RefSeq
RNA

About this Paper

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