PSIC: profile extraction from sequence alignments with position-specific counts of independent observations.

By Shamil R. Sunyaev, Frank Eisenhaber, I. Rodchenkov, B. Eisenhaber, V. Tumanyan, E. Kuznetsov. 1999

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Citations in the corpus

Quantitative missense variant effect prediction using large-scale mutagenesis data (2017, positive): “Several evolutionary features used in our model were obtained using the PolyPhen2 annotation pipeline (Sunyaev et al., 1999).”
Predicting Functional Effect of Human Missense Mutations Using PolyPhen-2 (2013, methodology): “Only used for sites that map to a 3-”
Tools for Predicting the Functional Impact of Nonsynonymous Genetic Variation (2016, methodology): “The second difference was in how amino acid probabilities were determined from the alignment: SIFT and PANTHER weighted each sequence equally at all positions in a given alignment (Henikoff and Henikoff 1994), while PolyPhen used position-speci ﬁ c sequence weighting (Sunyaev et al. 1999).”
Variation Interpretation Predictors: Principles, Types, Performance, and Choice (2016, background): “, 2013], and position-specific independent count scores [Sunyaev et al., 1999].”
SNAP predicts effect of mutations on protein function (2008, unknown): “Contact: bromberg@rostlab.org Supplementary information: Supplementary data are available at Bioinformatics online.”
COMPASS: a tool for comparison of multiple protein alignments with assessment of statistical significance. (2003, background): “counts (PSIC).(19) Residue content at each position is derived not from the overall weights for the sequences of the alignment but from the similarity of the sequence subset, which contains the given residue at the given position.”
Human non-synonymous SNPs: server and survey. (2002, methodology): “The set of aligned sequences with sequence identity to the input sequence in the range 30±94% (inclusive) is used by the new version of the PSIC (position-speci®c independent counts) software (24) to calculate the so-called pro®le matrix (http://strand.”
AL2CO: calculation of positional conservation in a protein sequence alignment (2001, methodology): “For a given alignment, we can calculate the value of F real (Sunyaev et al., 1999).”
PROMALS: towards accurate multiple sequence alignments of distantly related proteins (2007, background): “They are estimated from the position-specific independent counts (PSIC) of amino acids (Pei and Grishin, 2001; Sunyaev et al., 1999), which is a sequence-weighting scheme that corrects for biased similarities between sequences.”
Scoring residue conservation (2002, methodology): “A more elaborate method that considers each aligned column separately is the position-speciﬁc independent counts method of Sun-yaev et al. 39 More sophisticated weighting schemes based on entropy are described by May 40 and in Durbin et al. 10 Sibbald and Argos apply Voronoi diagrams to the problem ”
Prediction of deleterious human alleles. (2001, methodology): “In this study we used a new version of the PSIC (33) profile analysis program (http:// combio.”
Using bioinformatics to predict the functional impact of SNVs (2011, methodology): “For example, 4000 Escherichia coli lac repressor amino acid substitution mutants had been tested for their ability to repress β-galactosidase activity and respond to inducer, with a colorimetric assay (Markiewicz et al., 1994).”
SNAP: predict effect of non-synonymous polymorphisms on function (2007, methodology): “Shorter windows yielded slightly higher performance for some settings with the clear tendency of ‘shorter toward the protein surface.’ The input feature that had the most descriptive value for all three accessibility classes was the PSIC ( 3 ) conservation weight (Methods section).”