CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
5ANC_1 2NOI_1 7YDP_1 Letter Amino acid
18 0 6 H Histidine
4 0 8 W Tryptophan
27 3 19 A Alanine
9 0 6 D Aspartic acid
15 0 9 Q Glutamine
23 0 53 L Leucine
54 0 12 K Lycine
30 2 21 T Threonine
27 0 15 R Arginine
4 4 14 C Cysteine
22 0 11 E Glutamic acid
20 0 20 I Isoleucine
8 0 4 M Methionine
34 0 21 V Valine
11 0 6 N Asparagine
34 6 26 G Glycine
16 0 22 F Phenylalanine
12 0 5 P Proline
18 0 18 S Serine
12 0 11 Y Tyrosine 

5ANC_1|Chain A|60S RIBOSOMAL PROTEIN L3|DICTYOSTELIUM DISCOIDEUM (44689)
>2NOI_1|Chain A[auth B]|5'-D(*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*GP*C)-3'|
>7YDP_1|Chain A[auth R]|Adhesion G protein-coupled receptor E5 subunit beta|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 \(w=f(c)\)
5ANC , Knot 172 398 0.86 40 214 379 
MSHRKFEAPRHGNLGFRPRKRAARHQGKVKSFPKDDRTQKVHLTAFMGYKAGMTHVVRDLEKPGSKMHKKEIVEAVTIIECPPMYIVGLVGYVETAQGLKTYKTVWAQHLSDNFRRRLYKNWYKSKSKKAFTKYVKQYETEEGKKSIEASLQAIKKRCSVVRVIAHTQVHKLKLTQKKAHVLEIQVNGGSIVEKVNFAVANFEKTVNVTGVFAENELIDVIGVTKGKGFNGVIKRWGVRKLPRKTHKGLRKVACIGAWHPSRVSTTVPRAGQLGYHHRVERNKKIYRIGQAQPEDGKQISTGKTEFDLTEKTINPMGGFAHYGMVKHEFLMLKGCVAGPRKRALTLRKSITTQTGRAALEKITLKFIDTSSKFGHGLHQTAEDKTKYFGVKKSRSTKA
2NOI , Knot 9 15 0.54 8 11 12 
GGTAGACCTGGACGC
7YDP , Knot 131 307 0.81 40 180 293 
MSSFAILMAHYDVEDWKLTLITRVGLALSLFCLLLCILTFLLVRPIQGSRTTIHLHLCICLFVGSTIFLAGIENEGGQVGLRCRLVAGLLHYCFLAAFCWMSLEGLELYFLVVRVFQGQGLSTRWLCLIGYGVPLLIVGVSAAIYSKGYGRPRYCWLDFEQGFLWSFLGPVTFIILCNAVIFVTTVWKLTQKFSEINPDMKKLKKARALTITAIAQLFLLGCTWVFGLFIFDDRSLVLTYVFTILNCLQGAFLYLLHCLLNKKVREEYRKWACLVAGGSKYSEFTSTTSGTGHNQTRALRASESGIL

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 \(c\).

\(|P_{f(5ANC_1)}(2) \setminus P_{f(2NOI_1)}(2)|=207\), \(|P_{f(2NOI_1)}(2) \setminus P_{f(5ANC_1)}(2)|=4\). 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 1:10000101100101110100011000101001100000001010111100111001100100110010000110110110011101111110100101100000111001000100010001000000011000100000001000101010110000011011100010010100001011010101101100101111010001010111100011011110010110111001110011000001100110111101001000110110110000100000100110101001001001000101000010111111001110001111010111100011010001000010111001010110000011011000100000011100000001
Pair \(Z_2\) Length of longest common subsequence
5ANC_1,2NOI_1 211 2
5ANC_1,7YDP_1 150 5
2NOI_1,7YDP_1 173 2

Newick tree

 
[
	2NOI_1:10.63,
	[
		5ANC_1:75,7YDP_1:75
	]:27.63
]

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 \((0.85)(0.8)(\frac{413 }{\log_{20} 413}-\frac{15}{\log_{20}15})=128.\)
Status Protein1 Protein2 d d1/2
Query variables 5ANC_1 2NOI_1 167 86
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]