CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
5RWF_1 4IQY_1 1ZIN_1 Letter Amino acid
6 8 5 C Cysteine
29 18 22 G Glycine
7 4 10 M Methionine
38 12 2 S Serine
16 11 16 R Arginine
17 8 4 H Histidine
31 17 12 I Isoleucine
24 7 6 F Phenylalanine
20 7 9 P Proline
8 3 0 W Tryptophan
22 15 14 V Valine
37 21 14 E Glutamic acid
43 22 22 L Leucine
21 11 17 D Aspartic acid
17 15 8 N Asparagine
23 3 10 Q Glutamine
32 24 12 K Lycine
39 10 9 T Threonine
16 8 7 Y Tyrosine
17 16 18 A Alanine 

5RWF_1|Chain A|Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 1|Homo sapiens (9606)
>4IQY_1|Chains A, B|O-acetyl-ADP-ribose deacetylase MACROD2|Homo sapiens (9606)
>1ZIN_1|Chain A|ADENYLATE KINASE|Geobacillus stearothermophilus (1422)
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 \(w=f(c)\)
5RWF , Knot 195 463 0.86 40 252 447 
SMEQPEPDMITIFIGTWNMGNAPPPKKITSWFLSKGQGKTRDDSADYIPHDIYVIGTQEDPLSEKEWLEILKHSLQEITSVTFKTVAIHTLWNIRIVVLAKPEHENRISHICTDNVKTGIANTLGNKGAVGVSFMFNGTSLGFVNSHLTSGSEKKLRRNQNYMNILRFLALGDKKLSPFNITHRFTHLFWFGDLNYRVDLPTWEAETIIQKIKQQQYADLLSHDQLLTERREQKVFLHFEEEEITFAPTYRFERLTRDKYAYTKQKATGMKYNLPSWCDRVLWKSYPLVHVVCQSYGSTSDIMTSDHSPVFATFEAGVTSQFVSKNGPGTVDSQGQIEFLRCYATLKTKSQTKFYLEFHSSCLESFVKSQEGENEEGSEGELVVKFGETLPKLKPIISDPEYLLDQHILISIKSSDSDESYGEGCIALRLEATETQLPIYTPLTHHGELTGHFQGEIKLQTSQ
4IQY , Knot 108 240 0.82 40 168 233 
GHMKKKVWREEKERLLKMTLEERRKEYLRDYIPLNSILSWKEEMKGKGQNDEENTQETSQVKKSLTEKVSLYRGDITLLEVDAIVNAANASLLGGGGVDGCIHRAAGPCLLAECRNLNGCDTGHAKITCGYDLPAKYVIHTVGPIARGHINGSHKEDLANCYKSSLKLVKENNIRSVAFPCISTGIYGFPNEPAAVIALNTIKEWLAKNHHEVDRIIFCVFLEVDFKIYKKKMNEFFSVD
1ZIN , Knot 100 217 0.82 38 155 210 
MNLVLMGLPGAGKGTQAEKIVAAYGIPHISTGDMFRAAMKEGTPLGLQAKQYMDRGDLVPDEVTIGIVRERLSKDDCQNGFLLDGFPRTVAQAEALETMLADIGRKLDYVIHIDVRQDVLMERLTGRRICRNCGATYHLIFHPPAKPGVCDKCGGELYQRADDNEATVANRLEVNMKQMKPLVDFYEQKGYLRNINGEQDMEKVFADIRELLGGLAR

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 \(c\).

\(|P_{f(5RWF_1)}(2) \setminus P_{f(4IQY_1)}(2)|=127\), \(|P_{f(4IQY_1)}(2) \setminus P_{f(5RWF_1)}(2)|=43\). 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 1:0100101011011110101101111001001110010100000010011001011100001100001101100010010010100111001101011111010000010010000100111001100111110111010011110001001000010000001011011111000101101000100111110100010110101001100100000101100001100000001110100001011100010010000010000010110001101000111000111011000010000110000011110101110001100011101000101011000101000000010101000010011000010000100101110110011010111001001100011101000000000101011101010000111001100010101010101010000
Pair \(Z_2\) Length of longest common subsequence
5RWF_1,4IQY_1 170 4
5RWF_1,1ZIN_1 185 4
4IQY_1,1ZIN_1 155 4

Newick tree

 
[
	5RWF_1:92.29,
	[
		4IQY_1:77.5,1ZIN_1:77.5
	]:14.79
]

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 \((0.85)(0.8)(\frac{703 }{\log_{20} 703}-\frac{240}{\log_{20}240})=129.\)
Status Protein1 Protein2 d d1/2
Query variables 5RWF_1 4IQY_1 164 122
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]