CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
8BSX_1 1SKU_1 7KXR_1 Letter Amino acid
18 14 34 E Glutamic acid
15 15 18 I Isoleucine
25 38 23 L Leucine
20 20 12 S Serine
15 18 6 T Threonine
22 22 18 V Valine
28 34 15 A Alanine
12 15 5 R Arginine
19 16 14 N Asparagine
2 1 1 C Cysteine
17 14 12 Q Glutamine
19 15 12 G Glycine
20 14 33 K Lycine
4 8 4 M Methionine
16 12 8 F Phenylalanine
20 12 6 P Proline
5 2 0 W Tryptophan
25 21 19 D Aspartic acid
9 11 9 H Histidine
20 8 14 Y Tyrosine 

8BSX_1|Chain A|Isopenicillin N synthase|Aspergillus nidulans FGSC A4 (227321)
>1SKU_1|Chains A, C|Aspartate carbamoyltransferase catalytic chain|Escherichia coli (562)
>7KXR_1|Chain A[auth L]|Lethal factor|Bacillus anthracis (1392)
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 \(w=f(c)\)
8BSX , Knot 149 331 0.87 40 204 319 
MGSVSKANVPKIDVSPLFGDDQAAKMRVAQQIDAASRDTGFFYAVNHGINVQRLSQKTKEFHMSITPEEKWDLAIRAYNKEHQDQVRAGYYLSIPGKKAVESFCYLNPNFTPDHPRIQAKTPTHEVNVWPDETKHPGFQDFAEQYYWDVFGLSSALLKGYALALGKEENFFARHFKPDDTLASVVLIRYPYLDPYPEAAIKTAADGTKLSFEWHEDVSLITVLYQSNVQNLQVETAAGYQDIEADDTGYLINCGSYMAHLTNNYYKAPIDRVKWVNAERQSLPFFVNLGYDSVIDPFDPREPNGKSDREPLSYGDYLQNGLVSLINKNGQT
1SKU , Knot 139 310 0.85 40 190 299 
ANPLYQKHIISINDLSRDDLNLVLATAAKLKANPQPELLKHKVIASCFFEASTRTRLSFETSMHRLGASVVGFSDSANTSLGKKGETLADTISVISTYVDAIVMRHPQEGAARLATEFSGNVPVLNAGDGSNQHPTQTLLDLFTIQETQGRLDNLHVAMVGDLKYGRTVHSLTQALAKFDGNRFYFIAPDALAMPQYILDMLDEKGIAWSLHSSIEEVMAEVDILYMTRVQKERLDPSEYANVNAQFVLRASDLHNAKANMKVLHPLPRVDEIATDVDKTPHAWYFQQAGNGIFARQALLALVLNRDLVL
7KXR , Knot 114 263 0.80 38 159 251 
AGGHGDVGMHVKEKEKNKDENKRKDEERNKTQEEHLKEIMKHIVKIEVKGEEAVKKEAAEKLLEKVPSDVLEMYKAIGGKIYIVDGDITKHISLEALSEDKKKIKDIYGKDALLHEHYVYAKEGYCPVLVIQSSEDYVENTEKALNVYYEIGKILSRDILSKINQPYQKFLDVLNTIKNASDSDGQDLLFTNQLKEHPTDFSVEFLEQNSNEVQEVFAKAFAYYIEPQHRDVLQLYAPEAFNYMDKFNEQEINLSLEELKDQR

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 \(c\).

\(|P_{f(8BSX_1)}(2) \setminus P_{f(1SKU_1)}(2)|=92\), \(|P_{f(1SKU_1)}(2) \setminus P_{f(8BSX_1)}(2)|=78\). 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 1:1101001011010101111000110101100101100001110110011010010000001010101000101110100000000101100101110011001001010101001010100100010111000001110011000010111100111010111110000111001010001101111001010101011100110100101010001011011000010010100111000101000101100100110100000011100101101000011111011000110110100101000001100100100111011000100
Pair \(Z_2\) Length of longest common subsequence
8BSX_1,1SKU_1 170 4
8BSX_1,7KXR_1 163 3
1SKU_1,7KXR_1 151 4

Newick tree

 
[
	8BSX_1:85.70,
	[
		7KXR_1:75.5,1SKU_1:75.5
	]:10.20
]

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 \((0.85)(0.8)(\frac{641 }{\log_{20} 641}-\frac{310}{\log_{20}310})=91.9\)
Status Protein1 Protein2 d d1/2
Query variables 8BSX_1 1SKU_1 119 112.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]