@article{Georg:2018,
author = {Lott, Steffen C. and Schäfer, Richard A. and Mann, Martin and Backofen, Rolf and  Hess, Wolfgang R. and Voss, Björn and Georg, Jens},
title = {{GLASSgo} - Automated and reliable detection of {sRNA} homologs from a single input sequences},
journal = {Frontiers in Genetics},
year = {2018},
doi = {10.3389/fgene.2018.00124},
volume = {9},
user = {mmann},
pages = {124},
number = {},
issn = {1664-8021},
abstract = {Bacterial small RNAs (sRNAs) are important post-transcriptional regulators of 
            gene expression. The functional and evolutionary characterization of sRNAs 
            requires the identification of homologs, which is frequently challenging due 
            to their heterogeneity, short length and partly, little sequence conservation. 
            We developed the GLobal Automatic Small RNA Search go (GLASSgo) algorithm to 
            identify sRNA homologs in complex genomic databases starting from a single 
            sequence. GLASSgo combines an iterative BLAST strategy with pairwise identity 
            filtering and a graph-based clustering method that utilizes RNA secondary 
            structure information. We tested the specificity, sensitivity and runtime of 
            GLASSgo, BLAST and the combination RNAlien/cmsearch in a typical use case 
            scenario on 40 bacterial sRNA families. The sensitivity of the tested methods 
            was similar, while the specificity of GLASSgo and RNAlien/cmsearch was 
            significantly higher than that of BLAST. GLASSgo was on average about 87 times 
            faster than RNAlien/cmsearch, and only about 7.5 times slower than BLAST, 
            which shows that GLASSgo optimizes the trade-off between speed and accuracy in 
            the task of finding sRNA homologs. GLASSgo is fully automated, whereas BLAST 
            often recovers only parts of homologs and RNAlien/cmsearch requires extensive 
            additional bioinformatic work to get a comprehensive set of homologs. GLASSgo 
            is available as an easy-to-use web server to find homologous sRNAs in large 
            databases.}
}