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You are free: to share – to copy, distribute and transmit the work; to remix – to adapt the work; Under the following conditions: attribution – You must give appropriate credit, provide a link to the license, and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses ...
The HH-suite comes with a number of pre-built profile HMMs that can be searched using HHblits and HHsearch, among them a clustered version of the UniProt database, of the Protein Data Bank of proteins with known structures, of Pfam protein family alignments, of SCOP structural protein domains, and many more.
Significant increase in time to map reads with mismatches (or color errors). Uses an iterative version of the Rabin-Karp string search algorithm. Yes Free, GPL: SparkBWA Integrates the Burrows–Wheeler Aligner (BWA) on an Apache Spark framework running atop Hadoop. Version 0.2 of October 2016, supports the algorithms BWA-MEM, BWA-backtrack ...
Sequence clusters are often synonymous with (but not identical to) protein families. Determining a representative tertiary structure for each sequence cluster is the aim of many structural genomics initiatives.
The open-source software MMseqs is an alternative to BLAST/PSI-BLAST, which improves on current search tools over the full range of speed-sensitivity trade-off, achieving sensitivities better than PSI-BLAST at more than 400 times its speed. [27]
Using all the sample elements in all the selected clusters may be prohibitively expensive or unnecessary. Under these circumstances, multistage cluster sampling becomes useful. Instead of using all the elements contained in the selected clusters, the researcher randomly selects elements from each cluster. Constructing the clusters is the first ...
Consensus clustering is a method of aggregating (potentially conflicting) results from multiple clustering algorithms.Also called cluster ensembles [1] or aggregation of clustering (or partitions), it refers to the situation in which a number of different (input) clusterings have been obtained for a particular dataset and it is desired to find a single (consensus) clustering which is a better ...
The Hopkins statistic (introduced by Brian Hopkins and John Gordon Skellam) is a way of measuring the cluster tendency of a data set. [1] It belongs to the family of sparse sampling tests. It acts as a statistical hypothesis test where the null hypothesis is that the data is generated by a Poisson point process and are thus uniformly randomly ...