CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
6PUG_1 7FXC_1 6VLM_1 Letter Amino acid
15 10 9 S Serine
16 12 11 T Threonine
15 2 4 Y Tyrosine
13 6 15 A Alanine
14 11 7 D Aspartic acid
21 9 11 E Glutamic acid
17 11 17 G Glycine
13 2 13 H Histidine
12 8 15 I Isoleucine
25 5 9 L Leucine
11 14 12 K Lycine
4 2 2 C Cysteine
16 2 10 Q Glutamine
10 6 3 F Phenylalanine
16 17 15 V Valine
9 4 5 N Asparagine
7 5 4 M Methionine
9 2 4 W Tryptophan
14 6 5 R Arginine
14 1 6 P Proline 

6PUG_1|Chains A, C|Major histocompatibility complex class I-related gene protein|Homo sapiens (9606)
>7FXC_1|Chain A|Fatty acid-binding protein, adipocyte|Homo sapiens (9606)
>6VLM_1|Chains A, B|Integrase|Human immunodeficiency virus 1 (11676)
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 \(w=f(c)\)
6PUG , Knot 127 271 0.87 40 195 261 
MRTHSLRYFRLGVSDPIHGVPEFISVGYVDSHPITTYDSVTRQKEPRAPWMAENLAPDHWERYTQLLRGWQQMFKVELKRLQRHYNHSGSHTYQRMIGCELLEDGSTTGFLQYAYDGQDFLIFNKDTLSWLAVDNVAHTIKQAWEANQHELLYQKNWLEEECIAWLKRFLEYGKDTLQRTEPPLVRVNRKETFPGVTALFCKAHGFYPPEIYMTWMKNGEEIVQEIDYGDILPSGDGTYQAWASIELDPQSSNLYSCHVEHSGVHMVLQVP
7FXC , Knot 69 135 0.83 40 104 129 
GSHMCDAFVGTWKLVSSENFDDYMKEVGVGFATRKVAGMAKPNMIISVNGDVITIKSESTFKNTEISFILGQEFDEVTADDRKVKSTITLDGGVLVHVQKWDGKSTTIKRKREDDKLVVECVMKGVTSTRVYERA
6VLM , Knot 82 177 0.80 40 135 171 
MAHHHHHHLVPRGSMHGQVDSSPGIWQLDCTHLEGKVILVAVHVASGYIEAEVIPAETGQETAYFLLKLAGRWPVKTIHTDNGSNFTSTTVKAACWWAGIKQEDGIPYNPQSQGVVESMNKELKKIIGQVRDQAEHLKTAVQMAVFIHNHKRKGGIGGYSAGERIVDIIATDIQTKE

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 \(c\).

\(|P_{f(6PUG_1)}(2) \setminus P_{f(7FXC_1)}(2)|=134\), \(|P_{f(7FXC_1)}(2) \setminus P_{f(6PUG_1)}(2)|=43\). 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 1:1000010010111001101110110110100011000001000001011111001110010000011011001101010010000000100000011100110010001110010010011110000101111001100100110100001100001100001111001100100010000111101000001111011100101101101010110010011001001011101010001110101010000100001000110111011
Pair \(Z_2\) Length of longest common subsequence
6PUG_1,7FXC_1 177 3
6PUG_1,6VLM_1 170 3
7FXC_1,6VLM_1 155 3

Newick tree

 
[
	6PUG_1:89.64,
	[
		6VLM_1:77.5,7FXC_1:77.5
	]:12.14
]

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 \((0.85)(0.8)(\frac{406 }{\log_{20} 406}-\frac{135}{\log_{20}135})=81.6\)
Status Protein1 Protein2 d d1/2
Query variables 6PUG_1 7FXC_1 110 79.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]