(680g) Genome-Wide Conservation Profiling and Size Distribution Analysis of Intergenic Sequences in Prokaryotes Provide Insights to Refine sRNA Searches

­­­­            Interest
in the search of small RNAs (sRNAs) in bacteria have
significantly increased in recent years due to the important regulatory
functions that they are now known to be capable of exerting [1]. Development of
high-throughput methods (e.g. next-generation sequencing) and more
sophisticated computational algorithms has allowed rapid identification of
potential sRNA targets in a way that includes
complete genome coverage [2-5]. However, given their varying size (50-500nts)
and their potential genomic locations in the 5' and 3' untranslated
regions as well as in intergenic regions [6], identification
and validation of true functionally-active sRNAs have
been challenging.

In this study, we analyzed the distribution of profiled sRNAs in 10 different bacteria species using existing transcriptome data. All the intergenic
regions were analyzed by WU-BLAST to examine conservation levels relative to
other species within or outside their genus. We categorized all members of this
bacterial set into different classes according to the conservation patterns
that we observed. We will discuss our observations of the correlations between conservation
of intergenic regions and sRNA
abundance. We also analyzed the size distribution of all intergenic
regions in each organism. We will discuss the latter results as well as their
implications for refining the discovery and validation of sRNAs
in prokaryotes using combined computational and experimental methods. 

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