CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
4DGB_1 2QAF_1 8CTX_1 Letter Amino acid
15 19 10 F Phenylalanine
8 19 6 S Serine
1 0 0 W Tryptophan
5 7 2 R Arginine
12 21 2 E Glutamic acid
5 9 1 H Histidine
3 9 3 Q Glutamine
10 32 11 I Isoleucine
6 10 4 P Proline
9 15 3 A Alanine
6 17 4 D Aspartic acid
4 6 0 C Cysteine
2 26 4 Y Tyrosine
14 33 4 K Lycine
5 12 0 M Methionine
11 13 9 T Threonine
9 13 10 V Valine
10 40 2 N Asparagine
23 16 8 G Glycine
7 25 13 L Leucine 

4DGB_1|Chain A|TRIMCyp|Macaca mulatta (9544)
>2QAF_1|Chains A, B|Orotidine 5' monophosphate decarboxylase|Plasmodium falciparum (36329)
>8CTX_1|Chains A, B|Potassium channel protein|Bacillus cereus m1550 (526969)
Protein code \(c\) LZ-complexity \(\mathrm{LZ}(w)\) Length \(n=|w|\) \(\frac{\mathrm{LZ}(w)}{n /\log_{20} n}\) \(p_w(1)\) \(p_w(2)\) \(p_w(3)\) Sequence \(w=f(c)\)
4DGB , Knot 81 165 0.83 40 128 161 
MVNPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHRIIPGFMCQGGNFTHHNGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVEAMERFGSRNGKTSKKITIADCGQLE
2QAF , Knot 146 342 0.83 38 193 328 
MGSSHHHHHHSSGLVPRGSMGFKVKLEKRRNAINTCLCIGLDPDEKDIENFMKNEKENNYNNIKKNLKEKYINNVSIKKDILLKAPDNIIREEKSEEFFYFFNHFCFYIINETNKYALTFKMNFAFYIPYGSVGIDVLKNVFDYLYELNIPTILDMKINDIGNTVKNYRKFIFEYLKSDSCTVNIYMGTNMLKDICYDEEKNKYYSAFVLVKTTNPDSAIFQKNLSLDNKQAYVIMAQEALNMSSYLNLEQNNEFIGFVVGANSYDEMNYIRTYFPNCYILSPGIGAQNGDLHKTLTNGYHKSYEKILINIGRAITKNPYPQKAAQMYYDQINAILKQNMES
8CTX , Knot 51 96 0.80 34 76 93 
AKDKEFQVLFVLTILTLISGTIFYSTVEGLRPIDALYFSVVTLTTVGYGDFSPQTDFGKIFTILYIFIGIGLVFGFIHKLAVNVQLPSILSNLVPR

Let \(P_w(n)\) be the set of distinct subwords (intervals) in a word \(w\). Let \(p_w(n)\) be the cardinality of \(P_w(n)\). Let \(f(c)\) be the sequence in FASTA with 4-symbol Protein Data Bank code \(c\).

\(|P_{f(4DGB_1)}(2) \setminus P_{f(2QAF_1)}(2)|=60\), \(|P_{f(2QAF_1)}(2) \setminus P_{f(4DGB_1)}(2)|=125\). Let \( Z_k(x,y)=|P_x(k)\setminus P_y(k)|+|P_y(k)\setminus P_x(k)| \) be a LZ76 style (set of subwords) Jaccard distance numerator for \(P(k)\).Hydrophobic-polar version of Sequence 1:110101110111010111010101110011001001011001001110010010011111100110100001011001010010000111000111110110111000100111001000110100111101001101101100110001000001011001010
Pair \(Z_2\) Length of longest common subsequence
4DGB_1,2QAF_1 185 3
4DGB_1,8CTX_1 146 3
2QAF_1,8CTX_1 173 4

Newick tree

 
[
	2QAF_1:94.42,
	[
		4DGB_1:73,8CTX_1:73
	]:21.42
]

Let d be the Otu--Sayood distance d.
Let d1 be the Otu--Sayood distance d1. (This makes the 4TYN sequence AAAAAA a close match...)
A roughly speaking expected distance is \((0.85)(0.8)(\frac{507 }{\log_{20} 507}-\frac{165}{\log_{20}165})=99.9\)
Status Protein1 Protein2 d d1/2
Query variables 4DGB_1 2QAF_1 127 94
Was not able to put for d
Was not able to put for d1

In notation analogous to [Theorem 16, Kjos-Hanssen, Niraula and Yoon (2022)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]