What is PhastCons?
PhastCons is a hidden Markov model-based method that estimates the probability that each nucleotide belongs to a conserved element, based on the multiple alignment. It considers not just each individual alignment column, but also its flanking columns.
How do you interpret PhastCons scores?
The PhastCons score is a probability that each nucleotide belongs to a conserved element, whereas abs(phyloP) is the -log(p-value) under a null hypothesis of neutral evolution, and a negative sign indicates faster-than expected evolution, while positive values imply conservation.
What is a phyloP score?
phyloP scores measure evolutionary conservation at individual alignment sites. Interpretations of the scores are compared to the evolution that is expected under neutral drift. Positive scores — Measure conservation, which is slower evolution than expected, at sites that are predicted to be conserved.
What is GERP score?
The GERP score is defined as the reduction in the number of substitutions in the multi-species sequence alignment compared to the neutral expectation.
What is dbNSFP?
dbNSFP is a database developed for functional prediction and annotation of all potential non-synonymous single-nucleotide variants (nsSNVs) in the human genome. Its current version is based on the Gencode release 29 / Ensembl version 94 and includes a total of 84,013,490 nsSNVs and ssSNVs (splicing-site SNVs).
What does a high GERP score mean?
For example, a GERP score of 4 would mean there are 4 fewer substitutions at a particular site than what is expected based on the neutral rate of evolution across the phylogeny. GERP scores have been commonly used in evolutionary genomic studies across different species.
What is a Grantham score?
The Grantham score attempts to predict the distance between two amino acids, in an evolutionary sense. A lower Grantham score reflects less evolutionary distance. A higher Grantham score reflects a greater evolutionary distance.
What is the difference between SNV and SNP?
However, a SNP is when an aberration is expected at the position for any member in the species – for example, a well characterized allele. A SNV on the other hand is when there is a variation at a position that hasn’t been well characterized – for example, when it is only seen in one individual.
What is LRT score?
The likelihood ratio test (LRT) is a statistical test of the goodness-of-fit between two models. A relatively more complex model is compared to a simpler model to see if it fits a particular dataset significantly better. If so, the additional parameters of the more complex model are often used in subsequent analyses.
How does align GVGD work?
Align-GVGD requires an alignment. Predictions are found to be highly varied depending on the alignment used. Using highly divergent sequences in an alignment can introduce gaps and will result in all amino acids being classed as neutral at that position.
How do you cite Provean?
If you publish research that uses provean you have to cite it as follows: Choi Y, Chan AP (2015) PROVEAN web server: a tool to predict the functional effect of amino acid substitutions and indels. Bioinformatics 31(16): 2745-2747.
Is SNP A variant?
Single-nucleotide variant (SNV), also known as single-nucleotide polymorphism (SNP), is the variant of a single nucleotide that occurs at a specific genomic position.