CLOTU: An online pipeline for processing and clustering of 454 amplicon reads into OTUs followed by taxonomic annotation

<p>Abstract</p> <p>Background</p> <p>The implementation of high throughput sequencing for exploring biodiversity poses high demands on bioinformatics applications for automated data processing. Here we introduce <smcaps>CLOTU</smcaps>, an online and open access pipeline for processing 454 amplicon reads. C<smcaps>LOTU</smcaps> has been constructed to be highly user-friendly and flexible, since different types of analyses are needed for different datasets.</p> <p>Results</p> <p>In <smcaps>CLOTU</smcaps>, the user can filter out low quality sequences, trim tags, primers, adaptors, perform clustering of sequence reads, and run <smcaps>BLAST</smcaps> against NCBInr or a customized database in a high performance computing environment. The resulting data may be browsed in a user-friendly manner and easily forwarded to downstream analyses. Although <smcaps>CLOTU</smcaps> is specifically designed for analyzing 454 amplicon reads, other types of DNA sequence data can also be processed. A fungal ITS sequence dataset generated by 454 sequencing of environmental samples is used to demonstrate the utility of <smcaps>CLOTU</smcaps>.</p> <p>Conclusions</p> <p>C<smcaps>LOTU</smcaps> is a flexible and easy to use bioinformatics pipeline that includes different options for filtering, trimming, clustering and taxonomic annotation of high throughput sequence reads. Some of these options are not included in comparable pipelines. C<smcaps>LOTU</smcaps> is implemented in a Linux computer cluster and is freely accessible to academic users through the Bioportal web-based bioinformatics service (<url>http://www.bioportal.uio.no</url>).</p

Estimation of Potential Seismic Damage in Urban Areas

Large earthquakes are known to have significant damage potential in urban regions. Recently all over the world, efforts are made toward reduction of future probable damages. The first step in damage mitigation is the estimation of expected damage levels in buildings that are subjected to earthquakes with different intensities. Due to the inherent uncertainties involved in the analyses, estimation of seismic damage rates must be handled within a probabilistic framework. To assess the damage rates under different shaking levels, “seismic damage” needs to be quantified and measured in a standard manner. The most common approach to quantify seismic damage rates is to perform fragility analyses. Fragility is defined as the probability of a system reaching a limit state as a function of seismic intensity levels..