The sRNAscanner is a computational tool used to detect the intergenic small RNA specific transcriptional units (TU) in the completely sequenced bacterial genome. It used the positional weight matrix based genomic sliding (Hertz and Stormo, 1999) to identify the 'orphan' intergenic transcriptional signals. Identified potent signals were further parsed using the efficient coordinate algorithm to identify intergenic transcriptional units. Identified such TU were differentiated in to "non-coding" and "coding" based on the presence of ribosome binding site (RBS) and initiation codons.
The methodology is described in: Sridhar J, Narmada SR, Sabarinathan R, Ou H-Y, Deng Z, Sekar K, Rafi ZA, and Rajakumar K. (2010)
sRNAscanner: A Computational Tool for Intergenic Small RNA Detection in Bacterial Genomes.
PLoS ONE 5(8): e11970
The source code for sRNAscanner suite programs can be obtained from here.
Download and extract the latest sRNAscanner*.tar.gz in /home/folder.
A complete documentation and instruction for the users to run sRNAscanner is given in Readme.pdf.
Testing sRNAscanner with known E. coli K12-MG1655 sRNA data
Figure 1. Overlap between the sRNA predictions made by the sRNAscanner and previous studies. Known sRNA groups predicted by sRNAscanner in E. coli K12-MG1655 were shaded with gray colour. Intergenic transcriptional units for 66 out of the 92 known sRNAs in E. coli K12 were identified.
Dr. Z.A. Rafi
Centre of Excellence in Bioinformatics
School of Biotechnology
Madurai Kamaraj University
Madurai 625 021
Dr. K. Rajakumar
Department of Infection, Immunity and Inflammation
University of Leicester
Leicester LE1 7RH
Dr. K. Sekar
Supercomputer Education and Research Centre
(Centre of Excellence in Structural Biology and Bio-computing)
Indian Institute of Science
Bangalore 560 012
Sridhar, J and Rafi, Z.A. (2007). Small RNA identification in Enteroabcteriaceae using synteny and genomic backbone retention. OMICS11: 74-99.
Sridhar, J and Rafi, Z.A.(2007). Identification of novel genomic islands associated with small RNAs. In Silico Biol.7:601-611.
Sridhar, J and Rafi, Z.A. (2008). Functional annotations in bacterial genomes based on small RNA signatures. Bioinformation2:284-295.
Sridhar, J. Sathesh Kumar, S and Rafi, Z.A. (2008). Small RNA identification in Enteroabcteriaceae using synteny and genomic backbone retention II. OMICS13: 261-284.
Sridhar, J. Sekar, K and Rafi Z. A. (2009). CsrA interacting small RNAs in Haemophilus spp genomes: A theoretical analysis. Arch Microbiol.191: 451-459.