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.
Highlights
Small RNAs of less than 40 nucleotides in length, such public databases such as UCSC [4], NCBI [5] or Ensembl as microRNAs, small interfering RNAs [6]
Our knowledge Doing large-scale genomic analysis with them would be of mammalian small RNAs has advanced rapidly, the exhausting
Researchers will have to record the primary transcripts of most mammalian small RNAs overlapping ESTs and mRNAs manually if they want to remain to be determined
Summary
Small RNAs of less than 40 nucleotides (nt) in length, such public databases such as UCSC [4], NCBI [5] or Ensembl as microRNAs (miRNAs), small interfering RNAs [6]. Researchers will have to record the primary transcripts of most mammalian small RNAs overlapping ESTs and mRNAs manually if they want to remain to be determined. MiRBase has been updated with the biogenesis of small RNAs. It facilitates (a) identifying genomic features of known miRNAs [7], and piRNABank the regulatory regions such as transcription factor binding is built for human, mouse and rat piRNAs supporting sites (TFBS) and discovering upstream regulators in searches for overlapping genes and repeat elements [8].
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