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Interpretation of PAE values allows scientists to understand the level of confidence in the predicted structure of a protein: Lower PAE values between residue pairs from different domains indicate that the model predicts well-defined relative positions and orientations for those domains.
CS-BLAST greatly improves alignment quality over the entire range of sequence identities and especially for difficult alignments in comparison to regular BLAST and PSI-BLAST. PSI-BLAST (Position-Specific Iterated BLAST) runs at about the same speed per iteration as regular BLAST, but is able to detect weaker sequence similarities that are still ...
It is thus an arithmetic average of the absolute errors | | = | |, where is the prediction and the true value. Alternative formulations may include relative frequencies as weight factors. Alternative formulations may include relative frequencies as weight factors.
If a vector of predictions is generated from a sample of data points on all variables, and is the vector of observed values of the variable being predicted, with ^ being the predicted values (e.g. as from a least-squares fit), then the within-sample MSE of the predictor is computed as
The nucleotide counts used for base calling contain errors and bias, both due do the sequenced reads themselves, and the alignment process. This issue can be mitigated to some extent by sequencing to a greater depth of read coverage, however this is often expensive, and many practical studies require making inferences on low coverage data. [1]
This list of sequence alignment software is a compilation of software tools and web portals used in pairwise sequence alignment and multiple sequence alignment. See structural alignment software for structural alignment of proteins.
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Linear errors-in-variables models were studied first, probably because linear models were so widely used and they are easier than non-linear ones. Unlike standard least squares regression (OLS), extending errors in variables regression (EiV) from the simple to the multivariable case is not straightforward, unless one treats all variables in the same way i.e. assume equal reliability.