CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
2COZ_1 1KPD_1 4DTL_1 Letter Amino acid
15 12 23 G Glycine
4 0 9 H Histidine
8 0 20 I Isoleucine
5 0 32 L Leucine
8 0 23 P Proline
12 0 33 S Serine
6 6 36 A Alanine
10 0 17 D Aspartic acid
6 0 31 K Lycine
1 0 5 W Tryptophan
3 0 11 Y Tyrosine
7 0 22 V Valine
2 0 9 R Arginine
6 0 19 N Asparagine
1 11 1 C Cysteine
4 0 27 Q Glutamine
12 0 25 E Glutamic acid
0 0 9 M Methionine
8 0 15 F Phenylalanine
4 0 29 T Threonine 

2COZ_1|Chain A|centrosome-associated protein 350|Homo sapiens (9606)
>1KPD_1|Chain A|RNA PSEUDOKNOT APKA27G|
>4DTL_1|Chain A|VgrG protein|Vibrio cholerae (666)
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 \(w=f(c)\)
2COZ , Knot 61 122 0.80 38 99 116 
GSSGSSGVEHEQQVTESPSLASVPTADELFDFHIGDRVLIGNVQPGILRFKGETSFAKGFWAGVELDKPEGNNNGTYDGIAYFECKEKHGIFAPPQKISHIPENFDDYVDINEDEDSGPSSG
1KPD , Knot 14 32 0.50 8 13 25 
GGCGCAGUGGGCUAGCGCCACUCAAAGGCCCG
4DTL , Knot 166 396 0.83 40 214 372 
GAQPNLGRSTKATPDFPTHFPKSSIGIENELAGLVVAMPANSAQKFGYVKSAQGDALFMLTKDMNQGSYQRPPSLQDGKNYQNWQTHTVELVSYPCEMDDKAAVETRKQAMLWLATHFTTHIDQSNHQPLAPIQSEDGRFVIEITNAKHVIAAGNGISAESQGQTITMTPSGQQATVGVAAKGFGTSATPELRLLESAPWYQKSLKSQFASLTSAENLDDKELAANVFAYLTSIYLKTAELAKKFGIYINEWDPMSEQITPNANGLTDPKVKNAWEILPRTKPSKIVEILSKSDAKAVMKHIKPQLQSRYSESLSKNVFQYFQDGGEVAGHGINNATVGDKHSPELAILFEFRTVPNELQSYLPKTESTTKSEVKLLDQFDPMKRKTVIQQVESLV

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 \(c\).

\(|P_{f(2COZ_1)}(2) \setminus P_{f(1KPD_1)}(2)|=98\), \(|P_{f(1KPD_1)}(2) \setminus P_{f(2COZ_1)}(2)|=12\). 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 1:10010011000001000101101101001101011001111010111101010001101111110100101000100011101000000111111001001100100010100000011001
Pair \(Z_2\) Length of longest common subsequence
2COZ_1,1KPD_1 110 2
2COZ_1,4DTL_1 179 4
1KPD_1,4DTL_1 221 3

Newick tree

 
[
	4DTL_1:11.67,
	[
		2COZ_1:55,1KPD_1:55
	]:56.67
]

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 \((0.85)(0.8)(\frac{154 }{\log_{20} 154}-\frac{32}{\log_{20}32})=43.4\)
Status Protein1 Protein2 d d1/2
Query variables 2COZ_1 1KPD_1 59 35.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]