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Comparative genomics of small RNAs in bacterial genomes

By Stan Luban, Daisuke Kihara1

Purdue University

Supplemental Material for the paper: Comparative genomics of small RNAs in bacterial genomes. OMICS. 2007 Spring;11(1):58-73.

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Version 1.0 - published on 08 Mar 2013 doi:10.4231/D37659F6Q - cite this Archived on 25 Oct 2016

Licensed under CC0 1.0 Universal

Description

In recent years, various families of small non-coding RNAs (sRNAs) have been discovered by experimental and computational approaches, both in bacterial and eukaryotic genomes. Although most of them await elucidation of their function, it has been reported that some play important roles in gene regulation. Here we carried out comparative genomics analysis of possible sRNAs that are computationally identified in 30 bacterial genomes from gamma- and alpha-proteobacteria and Deinococcus radiodurans. Identified sRNAs are clustered by a complete-linkage clustering method to see conservation among the organisms. On average, sRNAs are found in approximately 30% of intergenic regions of each genome sequence. Of these, 25.7% are conserved among three or more organisms. Approximately 60% of the conserved sRNAs do not locate in orthologous intergenic regions, implying that sRNAs may be shuffled their positions in genomes. The current study implies that sRNAs may be involved in a more extensive range of functions in bacteria.

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The README file is a summary of methods used, statistics of results obtained, how to read result files below, and other information. : The intergenic_region_files.tar.gz file contains intergenic region sequences of the 30 genomes used in the study. : The sRNAs_by_family file is a small RNA list sorted by family. : The sRNAs_by_org_then_length file is a small RNA list sorted by source organism name, resolving those by length. : The sRNAs_by_org_then_score file is a small RNA list sorted by organism name, resovling those by score. : The Ecoli_benchmark_sRNAs.xls file is a set of experimentally verified sRNAs from 3 groups (CBMB, Hebrew, Wisc) used as benchmark (downloadable in Excel format). : The Datasets of Experimentally Verified SRNAs are: [http://dir2.nichd.nih.gov/nichd/cbmb/segr/e.coli.html http://dir2.nichd.nih.gov/nichd/cbmb/segr/e.coli.html], [http://nar.oxfordjournals.org/cgi/content/full/31/7/1813 http://nar.oxfordjournals.org/cgi/content/full/31/7/1813], [http://www.genome.wisc.edu/sequencing/k12.htm#rna http://www.genome.wisc.edu/sequencing/k12.htm#rna], [http://www.sanger.ac.uk/Software/Rfam/ http://www.sanger.ac.uk/Software/Rfam/]