CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
6MPQ_1 5EQO_1 5HSW_1 Letter Amino acid
21 4 20 E Glutamic acid
9 1 6 M Methionine
7 4 24 Y Tyrosine
15 5 34 V Valine
11 6 20 Q Glutamine
7 12 23 R Arginine
0 6 13 C Cysteine
24 7 29 K Lycine
12 9 37 S Serine
16 5 39 A Alanine
20 8 25 G Glycine
16 7 23 I Isoleucine
15 7 23 T Threonine
6 1 7 W Tryptophan
6 6 30 D Aspartic acid
4 6 14 H Histidine
22 6 45 L Leucine
9 5 30 F Phenylalanine
8 7 28 P Proline
17 9 18 N Asparagine 

6MPQ_1|Chain A|Beta-lactamase|Acinetobacter baumannii (470)
>5EQO_1|Chain A|Angiogenin|Homo sapiens (9606)
>5HSW_1|Chain A|ORF 37|Human herpesvirus 8 type M (435895)
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 \(w=f(c)\)
6MPQ , Knot 111 245 0.83 38 161 230 
FHISSQQHEKAIKSYFDEAQTQGVIIIKEGKNLSTYGNALARANKEYVPASTFKMLNALIGLENHKATTNEIFKWDGKKRTYPMWEKDMTLGEAMALSAVPVYQELARRTGLELMQKEVKRVNFGNTNIGTQVDNFWLVGPLKITPVQEVNFADDLAHNRLPFKLETQEEVKKMLLIKEVNGSKIYAKSGWGMGVTPQVGWLTGWVEQANGKKIPFSLNLEMKEGMSGSIRNEITYKSLENLGII
5EQO , Knot 63 121 0.83 40 101 118 
QDNSRYTHFLTQHYDAKPQGRDDRYCESIMRRRGLTSPCKDINTFIHGNKRSIKAICENKNGNPHRENLRISKSSFQVTTCKLHGGSPWPPCQYRATAGFRNVVVACENGLPVHLDQSIFR
5HSW , Knot 202 488 0.85 40 261 464 
GAMEATPTPADLFSEDYLVDTLDGLTVDDQQAVLASLSFSKFLKHAKVRDWCAQAKIQPSMPALRMAYNYFLFSKVGEFIGSEDVCNFFVDRVFGGVRLLDVASVYAACSQMNAHQRHHICCLVERATSSQSLNPVWDALRDGIISSSKFHWAVKQQNTSKKIFSPWPITNNHFVAGPLAFGLRCEEVVKTLLATLLHPDETNCLDYGFMQSPQNGIFGVSLDFAANVKTDTEGRLQFDPNCKVYSIKCRFKYTFAKMECDPIYAAYQRLYEAPGKLALKDFFYSISKPAVEYVGLGKLPSESDYLVAYDQEWEACPRKKRKLTPLHNLIRECILHNSTTESDVYVLTDPQDTRGQISIKARFKANLFVNVRHSYFYQVLLQSSIVEEYIGLDSGIPRLGSPKYYIATGFFRKRGYQDPVNCTIGGDALDPHVEIPTLLIVTPVYFPRGAKHRLLHQAANFWSRSAKDTFPYIKWDFSYLSANVPHSP

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 \(c\).

\(|P_{f(6MPQ_1)}(2) \setminus P_{f(5EQO_1)}(2)|=122\), \(|P_{f(5EQO_1)}(2) \setminus P_{f(6MPQ_1)}(2)|=62\). 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 1:10100000001100010010001111100100100010111010000111001011011111000010000110101000001110001011011110111100011000110110001001011000110010011111110101100101100110001110100000100111100101001010011111101011110111001010011101010100110101000100001001111
Pair \(Z_2\) Length of longest common subsequence
6MPQ_1,5EQO_1 184 3
6MPQ_1,5HSW_1 194 3
5EQO_1,5HSW_1 226 4

Newick tree

 
[
	5HSW_1:10.38,
	[
		6MPQ_1:92,5EQO_1:92
	]:17.38
]

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 \((0.85)(0.8)(\frac{366 }{\log_{20} 366}-\frac{121}{\log_{20}121})=74.9\)
Status Protein1 Protein2 d d1/2
Query variables 6MPQ_1 5EQO_1 94 71
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]