CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
7FSQ_1 6UQQ_1 7QHD_1 Letter Amino acid
9 23 32 E Glutamic acid
6 13 7 H Histidine
15 22 31 K Lycine
0 9 18 Y Tyrosine
9 13 23 Q Glutamine
16 17 43 G Glycine
13 24 48 L Leucine
1 2 14 W Tryptophan
12 22 31 V Valine
9 15 31 N Asparagine
3 5 7 C Cysteine
7 7 8 M Methionine
12 14 33 T Threonine
11 9 32 A Alanine
8 14 22 R Arginine
11 17 21 D Aspartic acid
25 20 26 I Isoleucine
8 10 37 F Phenylalanine
5 14 30 P Proline
15 15 35 S Serine 

7FSQ_1|Chains A, B, C, D|Syntenin-1|Homo sapiens (9606)
>6UQQ_1|Chains A, B|Septin-7|Homo sapiens (9606)
>7QHD_1|Chain A|Cholinesterase|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 \(w=f(c)\)
7FSQ , Knot 90 195 0.81 38 132 183 
SMAEIKQGIREVILCKDQDGKIGLRLKSIDNGIFVQLVQANSPASLVGLRFGDQVLQINGENCAGWSSDKAHKVLKQAFGEKITMTIRDRPFERTITMHKDSTGHVGFIFKNGKITSIVKDSSAARNGLLTEHNICEINGQNVIGLKDSQIADILSTSGTVVTITIMPAFIFEHIIKRMAPSIMKSLMDHTIPEV
6UQQ , Knot 129 285 0.85 40 193 277 
MGSSHHHHHHSQDPGFEFTLMVVGESGLGKSTLINSLFLTDLYSPEYPGPSHRIKKTVQVEQSKVLIKEGGVQLLLTIVDTPGFGDAVDNSNCWQPVIDYIDSKFEDYLNAESRVNRRQMPDNRVQCCLYFIAPSGHGLKPLDIEFMKRLHEKVNIIPLIAKADTLTPEECQQFKKQIMKEIQEHKIKIYEFPETDDEEENKLVKKIKDRLPLAVVGSNTIIEVNGKRVRGRQYPWGVAEVENGEHCDFTILRNMLIRTHMQDLKDVTNNVHYENYRSRKLAAVT
7QHD , Knot 218 529 0.86 40 265 503 
EDDIIIATKNGKVRGMQLTVFGGTVTAFLGIPYAQPPLGRLRFKKPQSLTKWSDIWNATKYANSCCQNIDQSFPGFHGSEMWNPNTDLSEDCLYLNVWIPAPKPKNATVLIWIYGGGFQTGTSSLHVYDGKFLARVERVIVVSMNYRVGALGFLALPGNPEAPGNMGLFDQQLALQWVQKNIAAFGGNPKSVTLFGESAGAASVSLHLLSPGSHSLFTRAILQSGSFNAPWAVTSLYEARNRTLNLAKLTGCSRENETEIIKCLRNKDPQEILLNEAFVVPYGTPLSVNFGPTVDGDFLTDMPDILLELGQFKKTQILVGVNKDEGTAFLVYGAPGFSKDNNSIITRKEFQEGLKIFFPGVSEFGKESILFHYTDWVDDQRPENYREALGDVVGDYNFICPALEFTKKFSEWGNNAFFYYFEHRSSKLPWPEWMGVMHGYEIEFVFGLPLERRDQYTKAEEILSRSIVKRWANFAKYGNPQETQNQSTSWPVFKSTEQKYLTLNTESTRIMTKLRAQQCRFWTSFFPKV

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 \(c\).

\(|P_{f(7FSQ_1)}(2) \setminus P_{f(6UQQ_1)}(2)|=54\), \(|P_{f(6UQQ_1)}(2) \setminus P_{f(7FSQ_1)}(2)|=115\). 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 1:011010011001110000010111010010011110110100110111101100110101000111000010011001110010101000110001010000010111110010100110000110011100001001010011110000110110001011010111111100110011101100110001101
Pair \(Z_2\) Length of longest common subsequence
7FSQ_1,6UQQ_1 169 3
7FSQ_1,7QHD_1 207 4
6UQQ_1,7QHD_1 160 4

Newick tree

 
[
	7FSQ_1:98.83,
	[
		6UQQ_1:80,7QHD_1:80
	]:18.83
]

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 \((0.85)(0.8)(\frac{480 }{\log_{20} 480}-\frac{195}{\log_{20}195})=83.0\)
Status Protein1 Protein2 d d1/2
Query variables 7FSQ_1 6UQQ_1 108 89.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]