In the last decade, studies have indicated that small RNA molecules produced from non-coding gene transcripts, plays an important role in regulation of gene expression. Not all genes of an organism in a cell are uni-vocally expressed. The activation and suppression depends on the need of the cell and is subjected to various regulatory mechanisms.

Antisense RNA occurs naturally. They are small RNA molecule representing a unique type of DNA transcript that comprises 19–23 nucleotides. They pair to target a specific complementary region to control their biological function hence regulating gene expression. They therefore play a crucial role in regulating gene expression at multiple levels, such as at replication, transcription,

microRNAs (miRNA) are class of small noncoding functional RNAs. The regulatory role of miRNA has been studied in a wide variety of biological processes. Evidences suggesting roles of variation in difference in gene regulation have been shown by many groups including Hu et al. (2008), Jazdzewski et al. (2008), Frazer et al. (2009), Jazdzewski et

148 potential motifs are identified by analysing thousands of small RNA SRA sequencing samples DREME Discriminative Regular Expression Motif Elicitation For further information on how to interpret these results or to get a copy of the MEME software please access http://meme.nbcr.net. If you use DREME in your research please cite the following paper: Timothy L.

A total of 2485 entries of Sequence Read Archive (SRA) from Human small RNAseq samples containing trillion of bases of total sum size 1.23 TB were retrieved and processed using SRA Toolkit. Adapter trimming and sequence quality filtering was done using ea-utils. The resulting filtered fastq files are indexed using in-house developed algorithm. The index files were compiled using using

With the advent of next generation sequencing in 2008, the volume of biological data is growing exponentially. The sequence data are retained by NCBI Sequence Read Archive (SRA) at National Institutes of Health’s (NIH), EBI Sequence Read Archive (ERA) at European Bioinformatics Institute (EBI) and DDBJ Sequence Read Archive (DRA) at DNA Data Bank of