This paper surveys methods for the quality evaluation of multiple sequence alignment based on databases of reference alignments. Several classes of reference alignments have been defined. Then, applicable qualit
the graph-based method than the alignment-based one [27] and the difference of software implementations, several principal factors have significant effects on the error correction performance for both methods: long read error rate, short read error rate, short read coverage, alignment criterion, and...
We use it to capture the traces and then we compare two OTF traces by applying our alignment methods. The resulting differential trace is written in OTF format. We visualize the trace in Vampir [5]. 5.1 AMG2006 AMG2006 [1, 6] is a parallel algebraic multigrid solver for linear systems ...
RIPCAL has multiple modes of operation involving different combinations of RIP index and alignment-based methods. RIPCAL can be run in either command-line or graphical modes and is Perl-based. It is also compiled as a Windows executable. Dependent on the analysis method, RIPCAL accepts sequence...
Methods Mol BiolMethods in Molecular BiologyRussell, D. J. (2014). GramAlign: Fast alignment driven by grammar-based phylogeny. Multiple Sequence Alignment Methods.Russell, D. J. (2014). GramAlign: Fast alignment driven by grammar-based phylogeny. Methods in Molecular Biology (Clifton, N.J.)...
We compared the “ground truth” with the variants called at all coverages of simulated reads from both the alignment-based and assembly-based processes to calculate the recall rates and precisions as described in the methods section. With the alignment-based variant calling, the number of true...
In particular, design-based research methods can help with the problem of methodological alignment: ensuring that the research methods we use actually test what we think they are testing. I argue that our current notions of rigor overemphasize certain types of rigor at the expense of others and ...
The methods used were as follows: decision trees (DT), one nearest neighbour (1-NN) and k-nearest neighbour (k-NN) approach, support vector machines (SVM), and partial least-square projections to latent structures (PLS). The first four methods induce non-linear models, whereas PLS is a ...
In this field, methods based on sequence alignments like BLASTP are the most commonly used tools by biologists and bioinformaticians. However, an incorrect choice for the e-value threshold advised to identify homology and subsequently spread GO terms, may originate predictors with very low ...
Structure embedding based methods represent entities as distributed vectors based on the relational structure of KG, which captures the structure information of entities. Entities in KG have multimodal attributes such as name, degree, and position, which describe different characteristics of entities and ...