CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
2XQC_1 7HEK_1 7VKM_1 Letter Amino acid
9 3 17 Q Glutamine
9 6 20 E Glutamic acid
10 13 11 K Lycine
2 5 13 F Phenylalanine
6 5 16 P Proline
4 16 5 N Asparagine
6 9 16 D Aspartic acid
5 2 11 M Methionine
5 6 12 T Threonine
10 15 24 A Alanine
2 3 6 C Cysteine
12 22 24 V Valine
5 6 17 H Histidine
8 7 14 Y Tyrosine
9 6 14 I Isoleucine
16 19 35 L Leucine
5 11 13 S Serine
3 0 6 W Tryptophan
6 2 25 R Arginine
8 13 27 G Glycine 

2XQC_1|Chains A, D|TRANSPOSASE|DEINOCOCCUS RADIODURANS (1299)
>7HEK_1|Chains A, B|Non-structural protein 3|Severe acute respiratory syndrome coronavirus 2 (2697049)
>7VKM_1|Chain A|Tyrosine-protein kinase receptor|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 \(w=f(c)\)
2XQC , Knot 72 140 0.84 40 113 138 
MTYVILPLEMKKGRGYVYQLEYHLIWCVKYRHQVLVGEVADGLKDILRDIAAQNGLEVITMEVMPDHVHLLLSATPQQAIPDFVKALKGASARRMFVAYPQLKEKLWGGNLWNPSYCILTVSENTRAQIQKYIESQHDKE
7HEK , Knot 80 169 0.81 38 119 162 
SMVNSFSGYLKLTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGALNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFL
7VKM , Knot 139 326 0.82 40 204 310 
MSYYHHHHHHDYDIPTTENLYFQGAMGSGIRVHHIKRRDIVLKWELGEGAFGKVFLAECHNLLPEQDKMLVAVKALKEASESARQDFQREAELLTMLQHQHIVRFFGVCTEGRPLLMVFEYMRHRDLNRFLRSHGPDAKLLAGGEDVAPGPLGLGQLLAVASQVAAGMVYLAGLHFVHRDLATRNCLVGQGLVVKIGDFGMSRDIYSTDYYRVGGRTMLPIRWMPPESILYRKFTTESDVWSFGVVLWEIFTYGKQPWYQLSNTEAIDCITQGRELERPRACPPEVYAIMRGCWQREPQQRHSIKDVHARLQALAQAPPVYLDVLG

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 \(c\).

\(|P_{f(2XQC_1)}(2) \setminus P_{f(7HEK_1)}(2)|=70\), \(|P_{f(7HEK_1)}(2) \setminus P_{f(2XQC_1)}(2)|=76\). 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 1:10011111010010101001000111010000011110110110011001110011011010111001011101010011101101101101001111010100011110110100011010000010100010000000
Pair \(Z_2\) Length of longest common subsequence
2XQC_1,7HEK_1 146 4
2XQC_1,7VKM_1 175 5
7HEK_1,7VKM_1 181 4

Newick tree

 
[
	7VKM_1:93.74,
	[
		2XQC_1:73,7HEK_1:73
	]:20.74
]

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 \((0.85)(0.8)(\frac{309 }{\log_{20} 309}-\frac{140}{\log_{20}140})=52.0\)
Status Protein1 Protein2 d d1/2
Query variables 2XQC_1 7HEK_1 64 60.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]