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This chapter discusses the Cluster Application Availability (CAA) framework.
The top scoring 500 models are clustered using the Rosetta Cluster application, as described in Gray et al. [41], with a cluster radius cutoff of 2 Å peptide backbone atom RMSD.
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Traditional distributed file systems do not provide clusters with strict single-system image, and cannot fully meet the cluster applications requirements, such as I/O performance, scalability, reliability, and availability.
With the popularity of cluster applications, successive parallel versions of some mainstream protein identification tools have been introduced.
Figure 2 Simplified workflow of clustering application.
Aligned sequences were assigned (97% identity) to OTU's (phylotype clusters) using the Complete Linkage Clustering application of the RDP pyrosequencing pipeline [35].
By applying the furthest neighbor approach using the Complete Linkage Clustering application of the RDP pyrosequencing pipeline, trimmed pyrosequencing sequences could be assigned to phylotype clusters of either 97% or 98% V4/V6 identity.
These are presented and discussed further in an effort to highlight the complex set of factors that are likely to arise in any clustering application (as detailed by Milligan and Cooper [ 25]).
Recognising the capability, Wiewiórka et al. [ 21] developed SPARKSEQ for high-throughput sequence data analysis and the Big Data Genomics (BDG) group recently demonstrated the strength of SPARK in a genomic clustering application using ADAM, a set of formats and APIs as well as processing stage implementations for genomic data [ 22].
The main objective in clustering applications is to group samples into clusters of similar features (e.g., the SPNs).
In a big number of control and clustering applications, higher accuracy has been proved using the IT2 fuzzy logic [27].
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