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Table 1 Nomenclature and abbreviations

From: Mutagenesis Objective Search and Selection Tool (MOSST): an algorithm to predict structure-function related mutations in proteins

Variable name

Description

Posterior cumulative distribution function for the values of the property Ω at position i, given the previously known group of n amino acids present in the multiple alignment at such position

C DF (Ω1,Ω2), n

Cumulative distribution function of the absolute difference between the variances of any two properties Ω1 and Ω2 for a random combination of n amino acids

CDF Ω, n

Cumulative distribution function for a random combination of n amino acids and a given property Ω

H 0

Null hypothesis in the hypothesis test for differences

H 1

Alternative hypothesis in the hypothesis test for differences

i

Position number in the multiple alignment

IDP

Invariable determinant position

j or k

Amino acid numbering sub-index

L

Total number of physicochemical properties considered in the MOSST analysis

M

Number of possible pairwise combinations (subsets having two elements) of properties

n

Number of amino acids in a multiple alignment position (without taking gaps into account)

N

Total number of positions in the multiple alignment

N(μ,σ)

Normal distribution function with unknown parameters μ(mean) and σ (variance)

n i

Number of amino acids in position i of the multiple alignment (without taking gaps into account)

nsSNP

Non-synonymous single nucleotide polymorphism

p' i,(Ω1,Ω2), n

= 1 - p i,(Ω1,Ω2), n

Level of significance of the null hypothesis H 0 for the difference of the variances of the properties Ω1 and Ω2 at position i of a multiple alignment containing n amino acids

p' i,(Ωr,Ωs), n

= 1 - p i,(Ωr,Ωs),n

Level of significance of the null hypothesis H 0 for the difference of the variances of the properties Ωr and Ωs at position i of a multiple alignment containing n amino acids

p' m

Value of the mth level of significance, obtained from the set of M levels of significance of the differences between variances for all the possible pairwise combinations of properties, sorted in ascending order, for a given position i of a multiple alignment

p (Ω1,Ω2)

Probability of getting a certain value or less for the absolute difference Δσ (Ω1,Ω2) between the variances of any two properties Ω1 and Ω2

Posterior probability distribution function for the values of the property Ω at position i, given the previously known group of n amino acids present in the multiple alignment at such position

P i

Global probability of the null hypothesis being true considering all the properties together at position i , i.e. probability of all the variances being equal at position i of a multiple alignment

p i,(Ω1,Ω2),n

Probability of getting a certain value or less for the absolute difference Δσ (Ω1,Ω2) between the variances of any two properties Ω1 and Ω2 at position i of a multiple alignment containing n amino acids

p i,(Ωr,Ωs),n

Probability of getting a certain value or less for the absolute difference Δσ (Ωr,Ωs) between the variances of any two properties Ωr and Ωs at position i of a multiple alignment containing n amino acids

p i,Ω,n

Cumulative probability of getting a certain value or less for the variance (σi,Ω,n) for a given property Ω in position i of a multiple alignment containing n amino acids

PMF Ω, n

Discrete probability mass function for a random combination of n amino acids and any given property Ω

p Ω

Cumulative probability of getting a certain value or less for the variance for a given property Ω

Q j,i

Global probability for the occurrence of the amino acid j considering all properties together at position i in the multiple alignment, i.e. probability of the amino acid j satisfying all the physicochemical requirements at position i

q j,i ,Ω,n+1or

Probability of the amino acid j (any of the 20 natural amino acids) to be present at position i (containing n amino acids in the multiple alignment analyzed) in a new protein not included in the multiple alignment, according to property Ω or Ω r

r or s

Property numbering sub-index

VDP

Variable determinant position

VIP

Variable irrelevant position

x

Unknown quantity or variable

Xi,Ω,j or

Measure, value or score of the physicochemical property Ω or Ω r for the amino acid j at position i of a multiple alignment

X Ω, j

Measure, value or score of the physicochemical property Ω for the amino acid j

Δσ (Ω1,Ω2)

Absolute difference between the variances of any two properties Ω1 and Ω2

Δσ i,(Ω1,Ω2),n

Absolute difference between the variances of any two properties Ω1 and Ω2 at position i of a multiple alignment containing n amino acids

Δσ i,(Ωr,Ωs),n

Absolute difference between the variances of any two properties Ωr and Ωs at position i of a multiple alignment containing n amino acids

μ

Mean (of a normal distribution)

μ i,Ω,n

Arithmetical average of the physicochemical property Ω in position i of the multiple alignment containing a number of n amino acids

μ Ω

Arithmetical average of the physicochemical property Ω

σ

Variance (of a normal distribution)

σ i,Ω,n

Sample variance estimator (standard deviation) of the physicochemical property Ω in position i of the multiple alignment containing a number of n amino acids

σ Ω

Sample variance estimator (standard deviation) of the physicochemical property Ω

τ i,Ω,n+1

Test statistic for the (n +1)th amino acid at position i of a multiple alignment containing n amino acids

Ω

Generic physicochemical property

Ω1, Ω2, Ω3

Physicochemical properties 1, 2 and 3

Ωr, Ωs or Ω r , Ω s

Physicochemical properties r and s