CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
1JBZ_1 8PEW_1 4UIG_1 Letter Amino acid
17 25 9 V Valine
12 31 7 I Isoleucine
13 21 1 N Asparagine
7 11 8 Q Glutamine
9 8 7 H Histidine
20 28 7 K Lycine
6 16 2 M Methionine
15 23 11 T Threonine
8 31 18 A Alanine
3 1 2 C Cysteine
16 36 10 E Glutamic acid
19 44 12 L Leucine
13 16 1 F Phenylalanine
1 1 0 W Tryptophan
11 7 2 Y Tyrosine
18 23 10 D Aspartic acid
23 29 11 G Glycine
10 17 2 P Proline
10 21 6 S Serine
7 30 10 R Arginine 

1JBZ_1|Chain A|GREEN FLUORESCENT PROTEIN|Aequorea victoria (6100)
>8PEW_1|Chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q[auth X], R[auth Y]|Transcription termination factor Rho|Escherichia coli (562)
>4UIG_1|Chain A|COPPER SENSITIVE OPERON REPRESSOR|STREPTOMYCES LIVIDANS (1916)
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 \(w=f(c)\)
1JBZ , Knot 109 238 0.83 40 159 225 
MSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTFTYGVQCFSRYPDHMKRHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSGNVYIMADKQKNGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSCQSALSKDPNEKRDHMVLLEFVTAAGITHGMDELYK
8PEW , Knot 177 419 0.85 40 219 405 
MNLTELKNTPVSELITLGENMGLENLARMRKQDIIFAILKQHAKSGEDIFGDGVLEILQDGFGFLRSADSSYLAGPDDIYVSPSQIRRFNLRTGDTISGKIRPPKEGERYFALLKVNEVNFDKPENARNKILFENLTPLHANSRLRMERGNGSTEDLTARVLDLASPIGRGQRGLIVAPPKAGKTMLLQNIAQSIAYNHPDCVLMVLLIDERPEEVTEMQRLVKGEVVASTFDEPASRHVQVAEMVIEKAKRLVEHKKDVIILLDSITRLARAYNTVVPASGKVLTGGVDANALHRPKRFFGAARNVEEGGSLTIIATALIDTGSKMDEVIYEEFKGTGNMELHLSRKIAEKRVFPAIDYNRSGTRKEELLTTQEELQKMWILRKIIHPMGEIDAMEFLINKLAMTKTNDDFFEMMKRS
4UIG , Knot 67 136 0.80 38 102 131 
GSHMTTTEAGASAPSPAVDGAVNQTARQAEADGTDIVTDHDRGVHGYHKQKAEHLKRLRRIEGQIRGLQRMVDEDVYCIDILTQVSASTKALQSFALQLLEEHLRHCVADAALKGGTEIDAKVEEATKAIGRLLRT

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 \(c\).

\(|P_{f(1JBZ_1)}(2) \setminus P_{f(8PEW_1)}(2)|=49\), \(|P_{f(8PEW_1)}(2) \setminus P_{f(1JBZ_1)}(2)|=109\). 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 1:1001001101111111010101010010101010101001010101100010111111011001001100100010010000110011101010000111000100000101010100110010101101000101110010000001010111000001101010100010010101100000001110111111000010000110001000000111101101111001100100
Pair \(Z_2\) Length of longest common subsequence
1JBZ_1,8PEW_1 158 4
1JBZ_1,4UIG_1 163 3
8PEW_1,4UIG_1 163 4

Newick tree

 
[
	4UIG_1:82.31,
	[
		1JBZ_1:79,8PEW_1:79
	]:3.31
]

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 \((0.85)(0.8)(\frac{657 }{\log_{20} 657}-\frac{238}{\log_{20}238})=117.\)
Status Protein1 Protein2 d d1/2
Query variables 1JBZ_1 8PEW_1 149 115.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]