CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
4XFQ_1 3CCM_1 1KHX_1 Letter Amino acid
8 4 6 M Methionine
20 23 13 A Alanine
20 9 13 N Asparagine
11 14 6 D Aspartic acid
10 13 12 E Glutamic acid
33 35 15 G Glycine
13 8 5 H Histidine
15 9 8 I Isoleucine
11 5 10 F Phenylalanine
13 23 13 R Arginine
8 2 9 C Cysteine
10 6 12 Q Glutamine
29 24 16 V Valine
24 11 22 S Serine
21 9 16 T Threonine
15 1 8 Y Tyrosine
27 10 20 L Leucine
7 15 4 K Lycine
6 18 14 P Proline
4 1 5 W Tryptophan 

4XFQ_1|Chains A, B|PEDV main protease|Porcine epidemic diarrhea virus (28295)
>3CCM_1|Chain A|50S ribosomal protein L2P|Haloarcula marismortui (2238)
>1KHX_1|Chain A|Smad2|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 \(w=f(c)\)
4XFQ , Knot 132 305 0.82 40 178 293 
AGLRKMAQPSGVVEKCIVRVCYGNMALNGLWLGDTVMCPRHVIASSTTSTIDYDYALSVLRLHNFSISSGNVFLGVVGVTMRGALLQIKVNQNNVHTPKYTYRTVRPGESFNILACYDGAAAGVYGVNMRSNYTIRGSFINGACGSPGYNINNGTVEFCYLHQLELGSGCHVGSDLDGVMYGGYEDQPTLQVEGASSLFTENVLAFLYAALINGSTWWLSSSRIAVDRFNEWAVHNGMTTVVNTDCFSILAAKTGVDVQRLLASIQSLHKNFGGKQILGYTSLTDEFTTGEVIRQMYGVHHHHHH
3CCM , Knot 104 240 0.79 40 142 224 
MGRRIQGQRRGRGTSTFRAPSHRYKADLEHRKVEDGDVIAGTVVDIEHDPARSAPVAAVEFEDGDRRLILAPEGVGVGDELQVGVSAEIAPGNTLPLAEIPEGVPVCNVESSPGDGGKFARASGVNAQLLTHDRNVAVVKLPSGEMKRLDPQCRATIGVVAGGGRTDKPFVKAGNKHHKMKARGTKWPNVRGVAMNAVDHPFGGGGRQHPGKPKSISRNAPPGRKVGDIASKRTGRGGNE
1KHX , Knot 105 227 0.83 40 169 221 
MDTGSPAELSPTTLSPVNHSLDLQPVTYSEPAFWCSIAYYELNQRVGETFHASQPSLTVDGFTDPSNSERFCLGLLSNVNRNATVEMTRRHIGRGVRLYYIGGEVFAECLSDSAIFVQSPNCNQRYGWHPATVCKIPPGCNLKIFNNQEFAALLAQSVNQGFEAVYQLTRMCTIRMSFVKGWGAEYRRQTVTSTPCWIELHLNGPLQWLDKVLTQMGSPSVRCSSMS

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 \(c\).

\(|P_{f(4XFQ_1)}(2) \setminus P_{f(3CCM_1)}(2)|=104\), \(|P_{f(3CCM_1)}(2) \setminus P_{f(4XFQ_1)}(2)|=68\). 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 1:11100110101110001101001011101111100110100111000000100001101101001010010111111110101111010100001001000000101100101110001111110110100000101011011010110010010101001001011010011001011101100001010101100110001111101111010011100001110010011100110011000010111100110100111010010001110011100010001001011001011000000
Pair \(Z_2\) Length of longest common subsequence
4XFQ_1,3CCM_1 172 3
4XFQ_1,1KHX_1 171 3
3CCM_1,1KHX_1 171 3

Newick tree

 
[
	3CCM_1:85.83,
	[
		4XFQ_1:85.5,1KHX_1:85.5
	]:0.33
]

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 \((0.85)(0.8)(\frac{545 }{\log_{20} 545}-\frac{240}{\log_{20}240})=86.9\)
Status Protein1 Protein2 d d1/2
Query variables 4XFQ_1 3CCM_1 111 97
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]