CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
3LCE_1 5MEP_1 7AVV_1 Letter Amino acid
18 24 18 A Alanine
18 20 18 G Glycine
8 12 36 P Proline
22 14 27 S Serine
6 14 17 Y Tyrosine
20 16 27 V Valine
6 18 15 D Aspartic acid
2 4 5 C Cysteine
10 17 19 Q Glutamine
4 5 9 M Methionine
11 23 24 T Threonine
7 10 5 W Tryptophan
23 22 54 E Glutamic acid
2 13 13 H Histidine
18 17 44 L Leucine
21 10 33 K Lycine
8 23 34 R Arginine
14 2 26 N Asparagine
16 4 39 I Isoleucine
12 8 24 F Phenylalanine 

3LCE_1|Chains A, B, C, D|Beta-lactamase OXA-10|Pseudomonas aeruginosa (287)
>5MEP_1|Chains A, D|HLA class I histocompatibility antigen, A-2 alpha chain|Homo sapiens (9606)
>7AVV_1|Chain A|Son of sevenless homolog 1|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 \(w=f(c)\)
3LCE , Knot 113 246 0.84 40 166 238 
SITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNDLARASKEYLPASTFKIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLTLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWLEGQLRISAVNQVEFLESLYLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKETEVYFFAFNMDIDNESKLPLRKSIPTKIMESEGIIGG
5MEP , Knot 122 276 0.82 40 182 264 
GSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEYWDGETRKVKAHSQTHRVDLGTLRGYYNQSEAGSHTVQRMYGCDVGSDWRFLRGYHQYAYDGKDYIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQLRAYLEGTCVEWLRRYLENGKETLQRTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGDGTFQKWAAVVVPSGQEQRYTCHVQHEGLPKPLTLRWEP
7AVV , Knot 200 487 0.84 40 246 459 
GEEQMRLPSADVYRFAEPDSEENIIFEENMQPKAGIPIIKAGTVIKLIERLTYHMYADPNFVRTFLTTYRSFCKPQELLSLIIERFEIPEPEPTEADRIAIENGDQPLSAELKRFRKEYIQPVQLRVLNVCRHWVEHHFYDFERDAYLLQRMEEFIGTVRGKAMKKWVESITKIIQRKKIARDNGPGHNITFQSSPPTVEWHISRPGHIETFDLLTLHPIEIARQLTLLESDLYRAVQPSELVGSVWTKEDKEINSPNLLKMIRHTTNLTLWFEKCIVETENLEERVAVVSRIIEILQVFQELNNFNGVLEVVSAMNSSPVYRLDHTFEQIPSRQKKILEEAHELSEDHYKKYLAKLRSINPPCVPFFGIYLTNILKTEEGNPEVLKRHGKELINFSKRRKVAEITGEIQQYQNQPYCLRVESDIKRFFENLNPMGNSMEKEFTDYLFNKSLEIEPRNPKPLPRFPKKYSYPLKSPGVRPSNPRPGT

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 \(c\).

\(|P_{f(3LCE_1)}(2) \setminus P_{f(5MEP_1)}(2)|=92\), \(|P_{f(5MEP_1)}(2) \setminus P_{f(3LCE_1)}(2)|=108\). 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 1:010000010001010110111110000000010001101000011100101101111100111000001101010101100100010101110101111100110011010100010010010001011100111010101011001011001010010100000111001110011100110000110111000011111111110000010111101010000011100011001100011111
Pair \(Z_2\) Length of longest common subsequence
3LCE_1,5MEP_1 200 4
3LCE_1,7AVV_1 178 3
5MEP_1,7AVV_1 196 4

Newick tree

 
[
	5MEP_1:10.12,
	[
		3LCE_1:89,7AVV_1:89
	]:13.12
]

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 \((0.85)(0.8)(\frac{522 }{\log_{20} 522}-\frac{246}{\log_{20}246})=78.9\)
Status Protein1 Protein2 d d1/2
Query variables 3LCE_1 5MEP_1 104 98
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]