Finding sRNA generative locales from high-throughput sequencing data with NiBLS

Background: Next-generation sequencing technologies allow researchers to obtain millions of sequence reads in a single experiment. One important use of the technology is the sequencing of small non-coding regulatory RNAs and the identification of the genomic locales from which they originate. Currently, there is a paucity of methods for finding small RNA generative locales. Results: We describe and implement an algorithm that can determine small RNA generative locales from highthroughput sequencing data. The algorithm creates a network, or graph, of the small RNAs by creating links between them depending on their proximity on the target genome. For each of the sub-networks in the resulting graph the clustering coefficient, a measure of the interconnectedness of the subnetwork, is used to identify the generative locales. We test the algorithm over a wide range of parameters using RFAM sequences as positive controls and demonstrate that the algorithm has good sensitivity and specificity...

• Type: Journal
• Year: 2010
• Where: BMCBI
• Authors: Daniel MacLean, Vincent Moulton, David J. Studholme
• Keywords: BMCBI 2010, Locales, Small Rna, Small Rna Generative