CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
6BCH_1 3TPT_1 1HHJ_1 Letter Amino acid
32 48 17 L Leucine
27 24 10 K Lycine
16 26 16 V Valine
14 38 24 A Alanine
10 13 17 Q Glutamine
8 25 11 P Proline
21 26 14 S Serine
21 24 23 T Threonine
4 6 10 W Tryptophan
18 24 18 D Aspartic acid
10 12 14 Y Tyrosine
31 30 4 I Isoleucine
3 11 5 M Methionine
17 30 23 R Arginine
21 18 2 N Asparagine
3 3 4 C Cysteine
20 25 22 E Glutamic acid
19 28 20 G Glycine
6 9 13 H Histidine
14 20 8 F Phenylalanine 

6BCH_1|Chains A, E[auth D], I[auth H], M[auth L]|Ribosomal protein 3/homing endonuclease-like fusion protein|Leptographium truncatum (330483)
>3TPT_1|Chains A, B|Serine/threonine-protein kinase HipA|Escherichia coli (562)
>1HHJ_1|Chains A, D|CLASS I HISTOCOMPATIBILITY ANTIGEN (HLA-A*0201) (ALPHA CHAIN)|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 \(w=f(c)\)
6BCH , Knot 137 315 0.83 40 188 298 
SYSTLANFPVQARNDNISPWTITGFADADSSFMLTVSKDSKRNTGWSVRPRFRIGLHNKDVTILKSIREYLGAGIITSDIDARIRFESLKELEVVINHFDKYPLITQKRADYLLFKKAFYLIKNKEHLTEEGLNQILTLKASLNLGLSEELKEAFPNTIPAERLLVTGQEIPDSNWVAGFTAGEGSFYIRIAKNSTLKTGYQVQSVFQITQDTRDIELMKNLISYLNCGNIRIRKYKGSEGIHDTCVDLVVTNLNDIKEKIIPFFNKNHIIGVKLQDYRDWCKVVTLIDNKEHLTSEGLEKIQKIKEGMNRGRSL
3TPT , Knot 184 440 0.84 40 237 424 
MPKLVTWMNNQRVGELTKLANGAHTFKYAPEWLASRYARPLSLSLPLQRGNITSDAVFNFFDNLLPDSPIVRDRIVKRYHAKSRQPFDLLSEIGRDSVGAVTLIPEDETVTHPIMAWEKLTEARLEEVLTAYKADIPLGMIREENDFRISVAGAQEKTALLRIGNDWCIPKGITPTTHIIKLPIGEIRQPNATLDLSQSVDNEYYCLLLAKELGLNVPDAEIIKAGNVRALAVERFDRRWNARRTVLLRLPQEDMCQTFGLPSSVKYESDGGPGIARIMAFLMGSSEALKDRYDFMKFQVFQWLIGATQGHAKNFSVFIQAGGSYRLTPFYDIISAFPVLGGTGIHISDLKLAMGLNASKGKKTAIDKIYPRHFLATAKVLRFPEVQMHEILSDFARMIPAALDNVKTSLPTDFPENVVTAVESNVLRLHGRLSREYGSK
1HHJ , Knot 122 275 0.83 40 182 263 
GSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEYWDGETRKVKAHSQTHRVDLGTLRGYYNQSEAGSHTVQRMYGCDVGSDWRFLRGYHQYAYDGKDYIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQLRAYLEGTCVEWLRRYLENGKETLQRTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGDGTFQKWAAVVVPSGQEQRYTCHVQHEGLPKPLTLRWE

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 \(c\).

\(|P_{f(6BCH_1)}(2) \setminus P_{f(3TPT_1)}(2)|=52\), \(|P_{f(3TPT_1)}(2) \setminus P_{f(6BCH_1)}(2)|=101\). 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 1:000011011101000010110101110100011101000000001101010101110000101100100011111100010101010010010111001000111000010011100110110000010001100110101010111000100111001110011101001100011111011010101011000010010010011010000001011001100100101010000100110000101110010010001111100001111010000010011011000001000110010010011001001
Pair \(Z_2\) Length of longest common subsequence
6BCH_1,3TPT_1 153 4
6BCH_1,1HHJ_1 206 4
3TPT_1,1HHJ_1 185 3

Newick tree

 
[
	1HHJ_1:10.04,
	[
		6BCH_1:76.5,3TPT_1:76.5
	]:27.54
]

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 \((0.85)(0.8)(\frac{755 }{\log_{20} 755}-\frac{315}{\log_{20}315})=120.\)
Status Protein1 Protein2 d d1/2
Query variables 6BCH_1 3TPT_1 152 128
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]