CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
4MKX_1 8BNB_1 4OGS_1 Letter Amino acid
21 5 18 D Aspartic acid
0 0 2 C Cysteine
21 6 7 Q Glutamine
5 2 11 Y Tyrosine
16 2 10 H Histidine
31 12 12 I Isoleucine
27 7 19 L Leucine
21 7 20 K Lycine
17 2 13 F Phenylalanine
18 12 9 S Serine
24 4 18 V Valine
12 4 7 R Arginine
13 2 13 N Asparagine
24 3 16 E Glutamic acid
10 2 6 M Methionine
8 2 10 P Proline
3 0 1 W Tryptophan
39 7 9 A Alanine
28 11 22 G Glycine
17 5 15 T Threonine 

4MKX_1|Chain A|Inositol dehydrogenase|Lactobacillus casei (543734)
>8BNB_1|Chains A, B|Leucine-rich repeat-containing protein 1|Trichoplax sp. H2 (287889)
>4OGS_1|Chains A, B|Green fluorescent protein|Aequorea victoria (6100)
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 \(w=f(c)\)
4MKX , Knot 152 355 0.83 38 202 337 
MRGSHHHHHHGSMTQKTIKIGIVGLGRLGKIHATNIATKIQHAKLQAATSVVPAELDWAKKELGVEEVFEDFDDMVQHADIDAVFIVSPSGFHLQQIESALNAGKHVFSEKPIGLDIEAIEHTQQVIAQHANLKFQLGFMRRFDDSYRYAKQLVDQGKIGDITLIRSYSIDPAAGMASFVKFATSANSGGLFLDMSIHDIDVIRWFTGKEIDKVWAIGLNRAYPVLDKAGELETGAALMQLEDKTMAILVAGRNAAHGYHVETEIIGTKGMLRIAQVPEKNLVTVMNEEGIIRPTSQNFPERFAQAFLSEEQAFVNSILNNQDVGITAEDGLQGTKAALALQEAFEKNDIVQVAS
8BNB , Knot 49 95 0.78 36 77 92 
GPLGSTIITSLQRKEGHSLGFSITGGFKQADGQYSGIYISKIAKDSIAAVDGKLSAGDILLKINDESMTNVPHSRAVQMLRSEGKIITIVASRQQ
4OGS , Knot 109 238 0.83 40 158 224 
MSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTFTYGVQCFSRYPDHMKRHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSVQAALSKDPNEKRDHMVLLEFVTAAGITHGMDELYK

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 \(c\).

\(|P_{f(4MKX_1)}(2) \setminus P_{f(8BNB_1)}(2)|=149\), \(|P_{f(8BNB_1)}(2) \setminus P_{f(4MKX_1)}(2)|=24\). 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 1:1010000000101000010111111101101010011001001010110011110101100011100110010011001010111110101101001001101100110001111010110000011100101010111100100000010011001011010110000101111110110110010011111010100101101101001001111110010111001101001111101000011111110011010010001110011101101100011011000111010000110011011100001110011000011101001101001111100110000110110
Pair \(Z_2\) Length of longest common subsequence
4MKX_1,8BNB_1 173 3
4MKX_1,4OGS_1 164 3
8BNB_1,4OGS_1 159 3

Newick tree

 
[
	4MKX_1:85.81,
	[
		4OGS_1:79.5,8BNB_1:79.5
	]:6.31
]

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 \((0.85)(0.8)(\frac{450 }{\log_{20} 450}-\frac{95}{\log_{20}95})=107.\)
Status Protein1 Protein2 d d1/2
Query variables 4MKX_1 8BNB_1 132 82.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]