CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
6WRR_1 7ODQ_1 2YTV_1 Letter Amino acid
15 10 1 P Proline
21 22 2 T Threonine
17 8 3 N Asparagine
43 40 4 L Leucine
27 15 3 I Isoleucine
28 62 3 A Alanine
20 21 4 D Aspartic acid
24 19 5 K Lycine
6 4 0 M Methionine
14 11 5 F Phenylalanine
5 3 1 W Tryptophan
30 21 6 E Glutamic acid
8 5 1 H Histidine
21 18 4 Q Glutamine
33 21 10 G Glycine
29 19 10 S Serine
9 8 1 Y Tyrosine
28 26 9 V Valine
14 16 4 R Arginine
8 3 3 C Cysteine 

6WRR_1|Chain A|Inositol polyphosphate 1-phosphatase|Bos taurus (9913)
>7ODQ_1|Chain A|Transaldolase|Neisseria gonorrhoeae (485)
>2YTV_1|Chain A|Cold shock domain-containing protein E1|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 \(w=f(c)\)
6WRR , Knot 175 400 0.87 40 228 388 
MSDILQELLRVSEKAANIARACRQQETLFQLLIEEKKEGEKNKKFAVDFKTLADVLVQEVIKENMENKFPGLGKKIFGEESNELTNDLGEKIIMRLGPTEEETVALLSKVLNGNKLASEALAKVVHQDVFFSDPALDSVEINIPQDILGIWVDPIDSTYQYIKGSADITPNQGIFPSGLQCVTVLIGVYDIQTGVPLMGVINQPFVSQDLHTRRWKGQCYWGLSYLGTNIHSLLPPVSTRSNSEAQSQGTQNPSSEGSCRFSVVISTSEKETIKGALSHVCGERIFRAAGAGYKSLCVILGLADIYIFSEDTTFKWDSCAAHAILRAMGGGMVDLKECLERNPDTGLDLPQLVYHVGNEGAAGVDQWANKGGLIAYRSEKQLETFLSRLLQHLAPVATHT
7ODQ , Knot 148 352 0.82 40 182 317 
GMTILSDVKALGQQIWLDNLSRSLVQSGELAQMLKQGVCGVTSNPAIFQKAFAGDALYADEVAALKRQNLSPKQRYETMAVADVRAACDVCLAEHESTGGKTGFVSLEVSPELAKDAQGTVEEARRLHAAIARKNAMIKVPATDAGIDALETLVSDGISVNLTLLFSRAQTLKAYAAYARGIAKRLAAGQSVAHIQVVASFFISRVDSALDATLPDRLKGKTAIALAKAAYQDWEQYFTAPEFAALEAQGANRVQLLWASTGVKNPAYPDTLYVDSLIGVHTVNTVPDATLKAFIDHGTAKATLTESADEARARLAEIAALGIDVETLAARLQEDGLKQFEEAFEKLLAPLV
2YTV , Knot 44 79 0.81 38 67 74 
GSSGSSGLRRATVECVKDQFGFINYEVGDSKKLFFHVKEVQDGIELQAGDEVEFSVILNQRTGKCSACNVWRVSGPSSG

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 \(c\).

\(|P_{f(6WRR_1)}(2) \setminus P_{f(7ODQ_1)}(2)|=105\), \(|P_{f(7ODQ_1)}(2) \setminus P_{f(6WRR_1)}(2)|=59\). 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 1:1001100110100011011010000001101110000010000011101001101110011000100011111001110000010001100111011100000111100110100110011101100011100111001010110011111101100000010101010100111101100101111100100111111110011100010000101000111001100100111110000000100010001000100010111000000010111001010011011111000101111110101100000101000110111011111110100010001001101101100110011111001100111110000001001100110011111000
Pair \(Z_2\) Length of longest common subsequence
6WRR_1,7ODQ_1 164 4
6WRR_1,2YTV_1 203 3
7ODQ_1,2YTV_1 173 3

Newick tree

 
[
	2YTV_1:98.05,
	[
		6WRR_1:82,7ODQ_1:82
	]:16.05
]

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 \((0.85)(0.8)(\frac{752 }{\log_{20} 752}-\frac{352}{\log_{20}352})=109.\)
Status Protein1 Protein2 d d1/2
Query variables 6WRR_1 7ODQ_1 142 130.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]