We believe alignment-based trace clustering provides results more useful for stakeholders. Moreover, in case of log incompleteness, noisy logs or concept drift, they can be more robust for dealing with highly d
We assembled the contigs based on their phred scores (15) using the Codon Code aligner v7.0.1, BioEdit and SeqTrace v0.9 software51. The contigs were checked for the presence of any chimeras in mothur v1.35.1 and were aligned for identification against the NCBI reference rRNA database usin...
the analysis than changing other preprocessing strategies. The clustering profiles were also highly similar between Chromap and CellRanger v2.0.0, no matter whether clustering was performed using the peak-based approach in MAESTRO or the bin-based approach in ArchR22(TableS4). On performance, ...
SortMeRNA is a local sequence alignment tool for filtering, mapping and clustering.The core algorithm is based on approximate seeds and allows for sensitive analysis of NGS reads. The main application of SortMeRNA is filtering rRNA from metatranscriptomic data. SortMeRNA takes as input files of reads...
Will S, Reiche K, Hofacker IL, Stadler PF, Backofen R: Inferring Noncoding RNA Families and Classes by Means of Genome-Scale Structure-Based Clustering. PLoS Comput Biol. 2007, 3 (4): e65-[http://dx.doi.org/10.1371/journal.pcbi.0030065] Article PubMed Central PubMed Google Scholar Ed...
Kececioglu [64, 63] introduced a graph-based formalization of multiple sequence alignment with sum-of-pairs cost function, the complete maximum-weight trace (CMWT) formalization. An ILP (integer linear programming) solution for this problem was presented in [84, 62]. In CMWT, the letters of...
the better alignment strategy leads to an order of magnitude speedup and error rates less than half of the current state-of-the-art for whole human genome data. As another application, we present a simple genotyping pipeline based on building a pangenome graph and aligning long reads to it....
The final multiple alignment at the root node is recovered in O(NL log N) time by storing the trace-back path at internal nodes and traversing the path from each leaf (input sequence) to the root. From this "first draft" multiple align- ment, the fractional identity of each pair of ...
We compared with ProtTrans and five structure-based methods: cliques, GRAFENE, ORCA, CNN (influenced by DeepFRI) and GCN (influenced by the Kipf and Welling GAE). Adjusted mutual information was computed by comparing spectral clustering assignments with structural label assignments for each CATH ...
the computer system uses backpropagation to trace the loss back from the output layer through the intermediate layers of the neural network to the input layer. The values of the weights associated with the connections between the nodes in the neural network are thereby updated. The error is back...