CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
2DWJ_1 6TIN_1 3VUW_1 Letter Amino acid
34 38 2 A Alanine
19 21 2 N Asparagine
13 11 6 Q Glutamine
6 21 1 H Histidine
11 17 2 F Phenylalanine
10 13 1 Y Tyrosine
20 7 0 C Cysteine
20 28 6 E Glutamic acid
25 40 6 G Glycine
33 42 9 L Leucine
27 24 7 K Lycine
21 30 3 S Serine
23 34 7 T Threonine
12 25 4 R Arginine
6 9 0 W Tryptophan
26 31 4 V Valine
21 33 5 D Aspartic acid
5 28 7 I Isoleucine
1 20 1 M Methionine
12 36 3 P Proline 

2DWJ_1|Chain A|Lactotransferrin|Bos taurus (9913)
>6TIN_1|Chain A[auth AAA]|Ferulic acid decarboxylase 1|Aspergillus niger (5061)
>3VUW_1|Chains A, B, C|Polyubiquitin-C|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 \(w=f(c)\)
2DWJ , Knot 146 345 0.82 40 199 326 
YTRVVWCAVGPEEQKKCQQWSQQSGQNVTCATASTTDDCIVLVLKGEADALNLDGGYIYTAGKCGLVPVLAENRKSSKHSSLDCVLRPTEGYLAVAVVKKANEGLTWNSLKDKKSCHTAVDRTAGWNIPMGLIVNQTGSCAFDEFFSQSCAPGADPKSRLCALCAGDDQGLDKCVPNSKEKYYGYTGAFRCLAEDVGDVAFVKNDTVWENTNGESTADWAKNLKREDFRLLCLDGTRKPVTEAQSCHLAVAPNHAVVSRSDRAAHVEQVLLHQQALFGKNGKNCPDKFCLFKSETKNLLFNDNTECLAKLGGRPTYEEYLGTEYVTAIANLKKCSTSPLLEACAF
6TIN , Knot 209 508 0.85 40 257 479 
MSAQPAHLCFRSFVEALKVDNDLVEINTPIDPNLEAAAITRRVCETNDKAPLFNNLIGMKNGLFRILGAPGSLRKSSADRYGRLARHLALPPTASMREILDKMLSASDMPPIPPTIVPTGPCKENSLDDSEFDLTELPVPLIHKSDGGKYIQTYGMHIVQSPDGTWTNWSIARAMVHDKNHLTGLVIPPQHIWQIHQMWKKEGRSDVPWALAFGVPPAAIMASSMPIPDGVTEAGYVGAMTGSSLELVKCDTNDLYVPATSEIVLEGTLSISETGPEGPFGEMHGYIFPGDTHLGAKYKVNRITYRNNAIMPMSSCGRLTDETHTMIGSLAAAEIRKLCQQNDLPITDAFAPFESQVTWVALRVDTEKLRAMKTTSEGFRKRVGDVVFNHKAGYTIHRLVLVGDDIDVYEGKDVLWAFSTRCRPGMDETLFEDVRGFPLIPYMGHGNGPAHRGGKVVSDALMPTEYTTGRNWEAADFNQSYPEDLKQKVLDNWTKMGFSNLEHHHHHH
3VUW , Knot 40 76 0.76 36 61 74 
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG

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 \(c\).

\(|P_{f(2DWJ_1)}(2) \setminus P_{f(6TIN_1)}(2)|=51\), \(|P_{f(6TIN_1)}(2) \setminus P_{f(2DWJ_1)}(2)|=109\). 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 1:000111011110000000010000100100101000000111110101011010110100110011111110000000000100110100101111110010011010010000000011000111011111110001001100110000111101000101101100011000110000000100111001100110111100001100001000101100100001011010100011001000011111001110000011010011100011110010001001011000000111000000110111010000011000101110100000011101011
Pair \(Z_2\) Length of longest common subsequence
2DWJ_1,6TIN_1 160 4
2DWJ_1,3VUW_1 186 3
6TIN_1,3VUW_1 230 3

Newick tree

 
[
	3VUW_1:11.57,
	[
		2DWJ_1:80,6TIN_1:80
	]:31.57
]

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 \((0.85)(0.8)(\frac{853 }{\log_{20} 853}-\frac{345}{\log_{20}345})=137.\)
Status Protein1 Protein2 d d1/2
Query variables 2DWJ_1 6TIN_1 174 143.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]