CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
4IUU_1 4IOC_1 3QXE_1 Letter Amino acid
6 2 4 N Asparagine
4 1 8 H Histidine
2 1 4 W Tryptophan
7 11 24 A Alanine
16 8 11 R Arginine
2 6 8 Q Glutamine
6 3 4 F Phenylalanine
9 7 11 S Serine
10 3 11 D Aspartic acid
7 8 20 G Glycine
4 9 7 I Isoleucine
3 8 8 K Lycine
0 3 8 M Methionine
5 3 8 Y Tyrosine
13 8 19 V Valine
6 0 3 C Cysteine
15 5 16 E Glutamic acid
13 3 20 L Leucine
3 3 18 P Proline
4 3 14 T Threonine 

4IUU_1|Chains A, B|SAWADEE HOMEODOMAIN HOMOLOG 1|Arabidopsis thaliana (3702)
>4IOC_19|Chain S[auth Q]|50S ribosomal protein L23|Deinococcus radiodurans (1299)
>3QXE_1|Chains A, C, E, G|Co-type Nitrile Hydratase alpha subunit|Pseudomonas putida (303)
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 \(w=f(c)\)
4IUU , Knot 68 135 0.82 38 113 132 
SADLAFEAKSARDYAWYDVSSFLTYRVLRTGELEVRVRFSGFDNRHDEWVNVKTSVRERSIPVEPSECGRVNVGDLLLCFQEREDQALYCDGHVLNIKRGIHDHARCNCVFLVRYELDNTEESLGLERICRRPEE
4IOC , Knot 52 95 0.83 38 77 93 
MSHYDILQAPVISEKAYSAMERGVYSFWVSPKATKTEIKDAIQQAFGVRVIGISTMNVPGKRKRVGRFIGQRNDRKKAIVRLAEGQSIEALAGQA
3QXE , Knot 103 226 0.82 40 155 216 
ASMTGGQQMGRGSEFMGQSHTHDHHHDGYQAPPEDIALRVKALESLLIEKGLVDPAAMDLVVQTYEHKVGPRNGAKVVAKAWVDPAYKARLLADGTAGIAELGFSGVQGEDMVILENTPAVHNVFVCTLCSCYPWPTLGLPPAWYKAAPYRSRMVSDPRGVLAEFGLVIPANKEIRVWDTTAELRYMVLPERPAGTEAYSEEQLAELVTRDSMIGTGLPTQPTPSH

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 \(c\).

\(|P_{f(4IUU_1)}(2) \setminus P_{f(4IOC_1)}(2)|=87\), \(|P_{f(4IOC_1)}(2) \setminus P_{f(4IUU_1)}(2)|=51\). 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 1:010111010010001100100110001100101010101011000000110100010000111010001010110111010000001100010110100110001000011110001000000111001000100
Pair \(Z_2\) Length of longest common subsequence
4IUU_1,4IOC_1 138 3
4IUU_1,3QXE_1 158 3
4IOC_1,3QXE_1 158 3

Newick tree

 
[
	3QXE_1:82.06,
	[
		4IUU_1:69,4IOC_1:69
	]:13.06
]

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 \((0.85)(0.8)(\frac{230 }{\log_{20} 230}-\frac{95}{\log_{20}95})=43.6\)
Status Protein1 Protein2 d d1/2
Query variables 4IUU_1 4IOC_1 57 47
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]