CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
2QEP_1 6NCL_1 2YXG_1 Letter Amino acid
15 24 9 D Aspartic acid
24 25 15 S Serine
23 24 31 V Valine
22 32 21 A Alanine
18 1 6 H Histidine
9 13 10 F Phenylalanine
13 11 7 Y Tyrosine
17 9 6 R Arginine
14 22 23 I Isoleucine
12 30 22 K Lycine
10 5 7 M Methionine
13 54 16 P Proline
17 24 19 N Asparagine
7 8 2 C Cysteine
11 7 3 Q Glutamine
23 20 31 E Glutamic acid
12 11 20 G Glycine
25 17 28 L Leucine
13 12 13 T Threonine
6 3 0 W Tryptophan 

2QEP_1|Chains A, B|Receptor-type tyrosine-protein phosphatase N2|Homo sapiens (9606)
>6NCL_1|Chain A[auth a0]|P14|Paramecium bursaria Chlorella virus 1 (10506)
>2YXG_1|Chains A, B, C, D|Dihydrodipicolinate synthase|Methanocaldococcus jannaschii DSM 2661 (243232)
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 \(w=f(c)\)
2QEP , Knot 134 304 0.84 40 201 292 
MSEEPVQSNMDISTGHMILSYMEDHLKNKNRLEKEWEALCAYQAEPNSSFVAQREENVPKNRSLAVLTYDHSRVLLKAENSHSHSDYINASPIMDHDPRNPAYIATQGPLPATVADFWQMVWESGCVVIVMLTPLAENGVRQCYHYWPDEGSNLYHIYEVNLVSEHIWCEDFLVRSFYLKNLQTNETRTVTQFHFLSWYDRGVPSSSRSLLDFRRKVNKCYRGRSCPIIVHCSDGAGRSGTYVLIDMVLNKMAKGAKEIDIAATLEHLRDQRPGMVQTKEQFEFALTAVAEEVNAILAHHHHHH
6NCL , Knot 123 352 0.68 40 173 255 
MQTPSIIQCGLLNSFARKMTDAISDNQIIATSRFFNIARDVADVVVSNTKLAQQYEQLSIDSLKEYLVSVAKFVAVDYSNTTSADVDDLIHKLRLFIEEECYQYNIDKEETCDGDVCVSDEYNEPAPKPKPKPKPKPAPKPKPAPKPKPAPKPAPKPAPKPAPKPAPKPAPKPAPKPAPEPAPEPAPEPAPKPAPEPAPEPAPIRPARRCDENPSNLETCCTNKALYGDFTDSSCDIVKKKTNWWLWGGIAILVIVLMIGGYFIYKRYFSAPKFENTGEFVNDMNFNNDVNFNNDVNFDNDMNYGNEGIDVSDLEILNLPVPSVSPVPSASIVPSVSPIPRGSPVPSASPIK
2YXG , Knot 126 289 0.82 38 171 280 
MFKGVYPAIITPFKNKEVDFDGLEENINFLIENGVSGIVAVGTTGESPTLSHEEHKKVIEKVVDVVNGRVQVIAGAGSNCTEEAIELSVFAEDVGADAVLSITPYYNKPTQEGLRKHFGKVAESINLPIVLYNVPSRTAVNLEPKTVKLLAEEYSNISAVKEANPNLSQVSELIHDAKITVLSGNDELTLPIIALGGKGVISVVANIVPKEFVEMVNYALEGDFEKAREIHYKLFPLMKAMFIETNPIPVKTALNMMGRPAGELRLPLCEMSEEHKKILENVLKDLGLI

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 \(c\).

\(|P_{f(2QEP_1)}(2) \setminus P_{f(6NCL_1)}(2)|=110\), \(|P_{f(6NCL_1)}(2) \setminus P_{f(2QEP_1)}(2)|=82\). 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 1:1000110001010010111001000100000100010110100101000111000001100001111000000111010000000001010111000100110110011111011011011100101111110111001100000011001001001001011000110001110010100100000001001011010001110000011010001000001000111100001110010011101110011011001011101001000011110000010111011100101111000000
Pair \(Z_2\) Length of longest common subsequence
2QEP_1,6NCL_1 192 4
2QEP_1,2YXG_1 170 4
6NCL_1,2YXG_1 150 3

Newick tree

 
[
	2QEP_1:95.31,
	[
		2YXG_1:75,6NCL_1:75
	]:20.31
]

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 \((0.85)(0.8)(\frac{656 }{\log_{20} 656}-\frac{304}{\log_{20}304})=97.7\)
Status Protein1 Protein2 d d1/2
Query variables 2QEP_1 6NCL_1 113 107
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]