CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
8CFJ_1 2GTH_1 3WAR_1 Letter Amino acid
21 24 15 N Asparagine
41 23 17 G Glycine
31 20 19 I Isoleucine
34 25 23 K Lycine
46 16 13 A Alanine
18 11 10 Q Glutamine
11 24 13 F Phenylalanine
7 4 5 W Tryptophan
12 11 23 Y Tyrosine
31 19 22 E Glutamic acid
12 7 16 H Histidine
16 10 15 P Proline
19 32 15 S Serine
15 5 11 M Methionine
27 14 11 T Threonine
35 39 26 V Valine
17 16 26 R Arginine
30 29 27 D Aspartic acid
8 9 2 C Cysteine
41 32 31 L Leucine 

8CFJ_1|Chains A, B, C, D|Adenosylhomocysteinase|Pseudomonas aeruginosa PAO1 (208964)
>2GTH_1|Chain A|Replicase polyprotein 1ab|Murine hepatitis virus (11142)
>3WAR_1|Chain A|Casein kinase II subunit alpha|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 \(w=f(c)\)
8CFJ , Knot 195 472 0.84 40 247 448 
SNAMSAVMTPAGFTDYKVADITLAAWGRRELIIAESEMPALMGLRRKYAGQQPLKGAKILGCIHMTIQTGVLIETLVALGAEVRWSSCNIFSTQDQAAAAIAAAGIPVFAWKGETEEEYEWCIEQTILKDGQPWDANMVLDDGGDLTEILHKKYPQMLERIHGITEETTTGVHRLLDMLKNGTLKVPAINVNDSVTKSKNDNKYGCRHSLNDAIKRGTDHLLSGKQALVIGYGDVGKGSSQSLRQEGMIVKVAEVDPICAMQACMDGFEVVSPYKNGINDGTEASIDAALLGKIDLIVTTTGNVNVCDANMLKALKKRAVVCNIGHFDNEIDTAFMRKNWAWEEVKPQVHKIHRTGKDGFDAHNDDYLILLAEGRLVNLGNATGHPSRIMDGSFANQVLAQIHLFEQKYADLPAAEKAKRLSVEVLPKKLDEEVALEMVKGFGGVVTQLTPKQAEYIGVSVEGPFKPDTYRY
2GTH , Knot 155 370 0.82 40 213 349 
SSLENVVYNLVNAGHFDGRAGELPCAVIGEKVIAKIQNEDVVVFKNNTPFPTNVAVELFAKRSIRPHPELKLFRNLNIDVCWSHVLWDYAKDSVFCSSTYKVCKYTDLQCIESLNVLFDGRDNGALEAFKKCRNGVYINTTKIKSLSMIKGPQRADLNGVVVEKVGDSDVEFWFAVRKDGDDVIFSRTGSLEPSHYRSPQGNPGGNRVGDLSGNEALARGTIFTQSRLLSSFTPRSEMEKDFMDLDDDVFIAKYSLQDYAFEHVVYGSFNQKIIGGLHLLIGLARRQQKSNLVIQEFVTYDSSIHSYFITDENSGSSKSVCTVIDLLLDDFVDIVKSLNLKCVSKVVNVNVDFKDFQFMLWCNEEKVMTF
3WAR , Knot 151 340 0.86 40 199 325 
GPLGSMSGPVPSRARVYTDVNTHRPREYWDYESHVVEWGNQDDYQLVRKLGRGKYSEVFEAINITNNEKVVVKILKPVKKKKIKREIKILENLRGGPNIITLADIVKDPVSRTPALVFEHVNNTDFKQLYQTLTDYDIRFYMYEILKALDYCHSMGIMHRDVKPHNVMIDHEHRKLRLIDWGLAEFYHPGQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRKEPFFHGHDNYDQLVRIAKVLGTEDLYDYIDKYNIELDPRFNDILGRHSRKRWERFVHSENQHLVSPEALDFLDKLLRYDHQSRLTAREAMEHPYFYTVVKDQARMG

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 \(c\).

\(|P_{f(8CFJ_1)}(2) \setminus P_{f(2GTH_1)}(2)|=96\), \(|P_{f(2GTH_1)}(2) \setminus P_{f(8CFJ_1)}(2)|=62\). 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 1:0011011101111000011010111110001111000111111100001100110110111010101001111001111110101000011000001111111111111110100000001010001100101101011100110100110000101100101100000011001101100101011110100010000000001000010011001000110100111110101101000010001111011010110110101011011010001100100101011111010111000101010010110110001110011010001001110001110010101001000100110100000111110101101101010100110101100111010110000101111001001010111001000111011011111100101001001110101110100000
Pair \(Z_2\) Length of longest common subsequence
8CFJ_1,2GTH_1 158 4
8CFJ_1,3WAR_1 164 4
2GTH_1,3WAR_1 172 4

Newick tree

 
[
	3WAR_1:85.63,
	[
		8CFJ_1:79,2GTH_1:79
	]:6.63
]

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 \((0.85)(0.8)(\frac{842 }{\log_{20} 842}-\frac{370}{\log_{20}370})=127.\)
Status Protein1 Protein2 d d1/2
Query variables 8CFJ_1 2GTH_1 160 141.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]