CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
3ICH_1 5CXF_1 3RGF_1 Letter Amino acid
7 37 21 R Arginine
1 11 6 C Cysteine
7 19 24 P Proline
12 45 16 T Threonine
5 40 14 N Asparagine
15 37 33 D Aspartic acid
25 25 23 G Glycine
3 16 19 H Histidine
10 37 22 I Isoleucine
25 30 40 K Lycine
7 57 18 S Serine
4 36 15 Y Tyrosine
8 36 22 A Alanine
3 14 11 M Methionine
14 30 17 F Phenylalanine
2 6 6 W Tryptophan
19 49 18 V Valine
2 23 17 Q Glutamine
11 38 24 E Glutamic acid
8 44 39 L Leucine 

3ICH_1|Chain A|Peptidyl-prolyl cis-trans isomerase B|Homo sapiens (9606)
>5CXF_1|Chains A, B, C|Envelope glycoprotein B|Human cytomegalovirus (10360)
>3RGF_1|Chain A|Cyclin-dependent kinase 8|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 \(w=f(c)\)
3ICH , Knot 88 188 0.81 40 136 182 
GPLGSDEKKKGPKVTVKVYFDLRIGDEDVGRVIFGLFGKTVPKTVDNFVALATGEKGFGYKNSKFHRVIKDFMIQGGDFTRGDGTGGKSIYGERFPDENFKLKHYGPGWVSMANAGKDTNGSQFFITTVKTAWLDGKHVVFGKVLEGMEVVRKVESTKTDSRDKPLKDVIIADCGKIEVEKPFAIAKE
5CXF , Knot 249 630 0.85 40 288 594 
YGDVVGVNTTKYPYRVCSMAQGTDLIRFERNIICTSMKPINEDLDEGIMVVYKRNIVAHTFKVRVYQKVLTFRRSYAGHRTTYLLGSNTEYVAPPMWEIHHINKFAQCYSSYSRVIGGTVFVAYHRDSHENKTMQLIPDDYSNTHSTRYVTVKDQWHSRGSTATHRETCNLNCMLTITTARSKYPYHFFATSTGDVVYISPFYNGTNRNASYFGENADKFFIFPNYTIVSDFGRPNAAPETHRLVAFLERADSVISWDIQDEKNVTCQLTFWEASERTIRSEAEDSYHFSSAKMTATFLSKKQEVNMSDSALDCVRDEAINKLQQIFNTSYNQTYEKYGNVSVFETSGGLVVFWQGIKQKSLVELERLANRSSLNITHDDDDKSTSDNNTTHLSSMESVHNLVYAQLQFTYDTLRGYINRALAQIAEAWCVDQRRTLEVFKELSKINPSAILSAIYNKPIAARFMGDVLGLASCVTINQTSVKVLRDMNVKESPGRCYSRPVVIFNFANSSYVQYGQLGEDNEILLGNHRTEECQLPSLKIFIAGNSAYEYVDYLFKRMIDLSSISTVDSMIALDIDPLENTDFRVLELYSQKELRSSNVFDLEEIMREFNSYKQRVKYVEDKVVDPLPP
3RGF , Knot 170 405 0.84 40 233 385 
DKMDYDFKVKLSSERERVEDLFEYEGCKVGRGTYGHVYKAKRKDGKDDKDYALKQIEGTGISMSACREIALLRELKHPNVISLQKVFLSHADRKVWLLFDYAEHDLWHIIKFHRASKANKKPVQLPRGMVKSLLYQILDGIHYLHANWVLHRDLKPANILVMGEGPERGRVKIADMGFARLFNSPLKPLADLDPVVVTFWYRAPELLLGARHYTKAIDIWAIGCIFAELLTSEPIFHCRQEDIKTSNPYHHDQLDRIFNVMGFPADKDWEDIKKMPEHSTLMKDFRRNTYTNCSLIKYMEKHKVKPDSKAFHLLQKLLTMDPIKRITSEQAMQDPYFLEDPLPTSDVFAGCQIPYPKREFLTEEEPDDKGDKKNQQQQQGNNHTNGTGHPGNQDSSHTQGPPLKK

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 \(c\).

\(|P_{f(3ICH_1)}(2) \setminus P_{f(5CXF_1)}(2)|=19\), \(|P_{f(5CXF_1)}(2) \setminus P_{f(3ICH_1)}(2)|=171\). 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 1:11110000001101010101010110001101111111001100100111110100111000001001100111011010010101100101001100010100011111011011000010011100100111010011110110110110010000000000110011110010101001111100
Pair \(Z_2\) Length of longest common subsequence
3ICH_1,5CXF_1 190 4
3ICH_1,3RGF_1 185 4
5CXF_1,3RGF_1 159 4

Newick tree

 
[
	3ICH_1:98.05,
	[
		3RGF_1:79.5,5CXF_1:79.5
	]:18.55
]

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 \((0.85)(0.8)(\frac{818 }{\log_{20} 818}-\frac{188}{\log_{20}188})=175.\)
Status Protein1 Protein2 d d1/2
Query variables 3ICH_1 5CXF_1 227 145
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]