CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
5YRF_1 2KJE_1 8GJN_1 Letter Amino acid
3 1 7 F Phenylalanine
4 0 5 W Tryptophan
8 4 5 A Alanine
7 0 7 D Aspartic acid
5 13 2 C Cysteine
2 5 1 H Histidine
9 5 10 V Valine
8 2 6 E Glutamic acid
11 4 4 I Isoleucine
7 7 11 L Leucine
10 6 19 S Serine
7 1 6 Y Tyrosine
8 7 5 R Arginine
4 5 3 N Asparagine
5 11 7 Q Glutamine
3 5 3 P Proline
11 2 14 T Threonine
17 3 13 G Glycine
12 10 7 K Lycine
1 1 3 M Methionine 

5YRF_1|Chain A|PPL3-A|Pteria penguin (113549)
>2KJE_1|Chain A|CREB-binding protein|Homo sapiens (9606)
>8GJN_1|Chain A|Heavy chain of 17B10 Fab|Mus musculus (10090)
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 \(w=f(c)\)
5YRF , Knot 68 142 0.79 40 113 137 
EIASEYLGGPGGDAFDDKAVAQNGDITRIEMQCTDVATYIKLRYGKVDSRQWGWGNENCIQWSKKGEKVVHELSSGEYITSAIVTYGKYVQSITFKTNKRTLPRCGTSATEKSVTVLIPGGLKYISGRWGCRIDGLRFHAKC
2KJE , Knot 50 92 0.82 36 78 89 
SPQESRRLSIQRCIQSLVHACQCRNANCSLPSCQKMKRVVQHTKGCKRKTNGGCPVCKQLIALCCYHAKHCQENKCPVPFCLNIKHKLRQQQ
8GJN , Knot 71 138 0.84 40 110 134 
MGWSWIFLFLLSGTAGVLSEVQLQQSGPELVKPGASVRISCKTSGYTFTEYSMFWVKQSHGQSLEWIGGINPNDDSTTYKQNFKGKATLTVDKSSSTAFMELRSLTSEDSAVYYCTRDRYDGRVVDFWGQGTTLTVSS

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 \(c\).

\(|P_{f(5YRF_1)}(2) \setminus P_{f(2KJE_1)}(2)|=81\), \(|P_{f(2KJE_1)}(2) \setminus P_{f(5YRF_1)}(2)|=46\). 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 1:0110001111110110001110010100101000011001010010100001111000010100010011001001001001110010010010100000011001001000010111111100101011001011010100
Pair \(Z_2\) Length of longest common subsequence
5YRF_1,2KJE_1 127 3
5YRF_1,8GJN_1 127 2
2KJE_1,8GJN_1 156 3

Newick tree

 
[
	8GJN_1:73.48,
	[
		5YRF_1:63.5,2KJE_1:63.5
	]:9.98
]

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 \((0.85)(0.8)(\frac{234 }{\log_{20} 234}-\frac{92}{\log_{20}92})=45.9\)
Status Protein1 Protein2 d d1/2
Query variables 5YRF_1 2KJE_1 55 45
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]