CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
7OKR_1 1PJG_1 7FCC_1 Letter Amino acid
17 0 6 Y Tyrosine
38 7 6 A Alanine
12 0 9 R Arginine
32 2 8 G Glycine
20 0 17 L Leucine
15 0 11 K Lycine
15 0 2 W Tryptophan
21 0 8 I Isoleucine
6 0 3 M Methionine
24 0 6 P Proline
28 0 4 N Asparagine
27 0 5 D Aspartic acid
4 1 2 C Cysteine
20 0 3 Q Glutamine
18 0 14 E Glutamic acid
7 0 3 H Histidine
15 0 8 F Phenylalanine
21 0 14 S Serine
30 0 4 T Threonine
25 0 13 V Valine 

7OKR_1|Chain A[auth AAA]|Chitinase B|Aliivibrio salmonicida (strain LFI1238) (316275)
>1PJG_1|Chain A|5'-R(*CP*AP*AP*AP*GP*AP*AP*AP*AP*G)-3'|
>7FCC_1|Chain A|Isoform 4 of Interleukin-1 receptor accessory protein|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 \(w=f(c)\)
7OKR , Knot 170 395 0.85 40 230 375 
MTNTIKINSLTIAFVGALSSMGVQAHGWVEYPSARQNTCYLDGGFWDNTIPNQACQSAFDESGAFPFVQRNEVAANVPNYKDMAHVQAIVRDGNLCSAGDKAKSGLNMGSTHWQKTAITLDENNQLELVFNATAPHNPSYWQFYLSNVNYDPTVPLTWGDLDVVDTAGDIIVGDDKKYRIKITLPADRADSAVLYTRWQREDAAGEGFYNCSDIAFDGAGTTPPGPIDPVEPPPQYSDLGYYIGQGFGPVESGDSVRFRTFDATGAETTDISLAITVNNTATWSAELAGQFNQLKNKAWFIGIWHQEMNHYMYDTINIYANRVFAPKANLSYQLSLIKADITPPVEPPVEPTNQWDKNNAYQARESVTHQGGTWVAQWWTKGEEPGKTGEWGVWR
1PJG , Knot 5 10 0.38 6 4 5 
CAAAGAAAAG
7FCC , Knot 69 146 0.78 40 111 141 
KEYDIYVSYARNAEEEEFVLLTLRGVLENEFGYKLCIFDRDSLPGGNTVEAVFDFIQRSRRMIVVLSPDYVTEKSISMLEFKLGVMCQNSIATKLIVVEYRPLEHPHPGILQLKESVSFVSWKGEKSKHSGSKFWKALRLALPLRS

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 \(c\).

\(|P_{f(7OKR_1)}(2) \setminus P_{f(1PJG_1)}(2)|=227\), \(|P_{f(1PJG_1)}(2) \setminus P_{f(7OKR_1)}(2)|=1\). 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 1:10001010010111111100111010111001010000001011110001100100011000111111000011101100001101011100101001100100110110001000110100000101110101100100101010010001011101101011001101111000000101011100100111000100001110110000011101110011111011011100001100110111110010010100101011000010111010001010101110100100011111110001000100010101001111010100010110101011101110100010000100100010001101110110010011001011110
Pair \(Z_2\) Length of longest common subsequence
7OKR_1,1PJG_1 228 3
7OKR_1,7FCC_1 201 3
1PJG_1,7FCC_1 115 1

Newick tree

 
[
	7OKR_1:11.56,
	[
		7FCC_1:57.5,1PJG_1:57.5
	]:62.06
]

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 \((0.85)(0.8)(\frac{405 }{\log_{20} 405}-\frac{10}{\log_{20}10})=128.\)
Status Protein1 Protein2 d d1/2
Query variables 7OKR_1 1PJG_1 168 85.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]