CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
7HUS_1 8ZBH_1 1FUJ_1 Letter Amino acid
6 11 12 T Threonine
14 20 20 V Valine
10 11 16 A Alanine
5 10 16 Q Glutamine
12 17 20 L Leucine
2 15 2 K Lycine
14 21 12 S Serine
9 10 10 D Aspartic acid
9 10 13 R Arginine
5 7 10 N Asparagine
2 6 3 M Methionine
4 10 16 P Proline
3 14 12 F Phenylalanine
3 1 3 W Tryptophan
8 11 3 Y Tyrosine
6 2 8 C Cysteine
7 17 4 E Glutamic acid
14 10 18 G Glycine
6 8 10 H Histidine
5 10 13 I Isoleucine 

7HUS_1|Chain A|Protease 2A|Coxsackievirus A16 (31704)
>8ZBH_1|Chains A, B, C|Transcriptional enhancer factor TEF-5|Homo sapiens (9606)
>1FUJ_1|Chains A, B, C, D|PR3|Homo sapiens (9606)
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 \(w=f(c)\)
7HUS , Knot 70 144 0.80 40 112 139 
SGAIYVGNYRVVNRHLATHNDWANLVWEDSSRDLLVSSTTAQGCDTIARCDCQTGVYYCSSRRKHYPVSFSKPSLIFVEASEYYPARYQSHLMLAVGHSEPGDCGGILRCQHGVVGIVSTGGNGLVGFADVRDLLWLDEEAMEQ
8ZBH , Knot 101 221 0.82 40 155 213 
SQDRTIASSRLRLLEYSAFMEVQRDPDTYSKHLFVHIGQTNPAFSDPPLEAVDVRQIYDKFPEKKGGLKELYEKGPPNAFFLVKFWADLNSTIQEGPGAFYGVSSQYSSADSMTISVSTKVCSFGKQVVEKVETEYARLENGRFVYRIHRSPMCEYMINFIHKLKHLPEKYMMNSVLENFTILQVVTSRDSQETLLVIAFVFEVSTSEHGAQHHVYKLVKD
1FUJ , Knot 102 221 0.83 40 158 215 
IVGGHEAQPHSRPYMASLQMRGNPGSHFCGGTLIHPSFVLTAAHCLRDIPQRLVNVVLGAHNVRTQEPTQQHFSVAQVFLNNYDAENKLNDILLIQLSSPANLSASVATVQLPQQDQPVPHGTQCLAMGWGRVGAHDPPAQVLQELNVTVVTFFCRPHNICTFVPRRKAGICFGDSGGPLICDGIIQGIDSFVIWGCATRLFPDFFTRVALYVDWIRSTLR

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 \(c\).

\(|P_{f(7HUS_1)}(2) \setminus P_{f(8ZBH_1)}(2)|=64\), \(|P_{f(8ZBH_1)}(2) \setminus P_{f(7HUS_1)}(2)|=107\). 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 1:011101100011000110000110111000000111000010100011000000110000000000110100101111010000110000011111100011001111000011111100110111111010011110001100
Pair \(Z_2\) Length of longest common subsequence
7HUS_1,8ZBH_1 171 3
7HUS_1,1FUJ_1 158 3
8ZBH_1,1FUJ_1 185 3

Newick tree

 
[
	8ZBH_1:92.18,
	[
		7HUS_1:79,1FUJ_1:79
	]:13.18
]

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 \((0.85)(0.8)(\frac{365 }{\log_{20} 365}-\frac{144}{\log_{20}144})=67.0\)
Status Protein1 Protein2 d d1/2
Query variables 7HUS_1 8ZBH_1 83 69.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]