CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
4MPQ_1 3NSP_1 1WFS_1 Letter Amino acid
29 11 8 G Glycine
14 12 5 I Isoleucine
15 10 6 F Phenylalanine
15 14 8 P Proline
17 15 15 S Serine
10 4 5 Y Tyrosine
19 12 9 D Aspartic acid
11 6 6 Q Glutamine
16 20 15 E Glutamic acid
15 13 12 K Lycine
13 11 8 T Threonine
9 9 4 N Asparagine
5 4 3 C Cysteine
29 33 14 L Leucine
3 2 1 W Tryptophan
43 22 5 A Alanine
13 8 1 H Histidine
11 8 4 M Methionine
27 14 13 V Valine
15 12 9 R Arginine 

4MPQ_1|Chain A|Dihydrodipicolinate synthetase|Brucella melitensis (546272)
>3NSP_1|Chains A, B|Retinoid X receptor, alpha|Homo sapiens (9606)
>1WFS_1|Chain A|Glia maturation factor gamma|Mus musculus (10090)
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 \(w=f(c)\)
4MPQ , Knot 142 329 0.83 40 194 312 
MAHHHHHHMLKAEIFSGVIPALMTPCKPDRSPDFDALVRKGQELIGDGMSAVVYCGSMGDWPLLTDAQRMEGVERLVKAGIPVIVGTGAVNTASAVAHAAHAQKVGAKGLMVIPRVLSRGSAIAAQKAYFKAILSAAPDLPAVIYNSPYYGFATRADLFFDLRAEHPNLVGFKEFGGPADMRYAAENITSRDDGVSLMIGVDTAVFHGFVNCGATGAITGIGNVLPKEVIHLCNLSQAAALGDVDARQRAQELEQALAVLSSFDEGPDLVLYFKHMMVLKGDKEYTLHFNETDALSESQRGYVETQFRLFNTWYAEWSKLPGAVQRCKA
3NSP , Knot 111 240 0.84 40 168 228 
TSSANEDMPVERILEAELAVEPKTETYVEANMGLNPSSPNDPVTNICQAADKQLFTLVEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAVKDGILLATGLHVHRNSAHSAGVGAIFDRVLTELVSKMRDMQMDKTELGCLRAIVLFNPDSKGLSNPAEVEALREKVYASLEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFFFKLIGDTPIDTFLMEMLEAPHQMT
1WFS , Knot 70 151 0.77 40 112 142 
GSSGSSGSDSLVVCEVDPELKETLRKFRFRKETNNAAIIMKVDKDRQMVVLEDELQNISPEELKLELPERQPRFVVYSYKYVHDDGRVSYPLCFIFSSPVGCKPEQQMMYAGSKNRLVQTAELTKVFEIRTTDDLTETWLKEKLASGPSSG

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 \(c\).

\(|P_{f(4MPQ_1)}(2) \setminus P_{f(3NSP_1)}(2)|=88\), \(|P_{f(3NSP_1)}(2) \setminus P_{f(4MPQ_1)}(2)|=62\). 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 1:11000000110101101111111010010001010111001001110110111001011011110010010110011011111111011100101110110100111011111101100101111001010111011101111100010011100101110101001011110011111010011001000001101111100111011100110111011101110011010010011111010100010010011111001001101110100111101000001010000110000010100010110010101001111100001
Pair \(Z_2\) Length of longest common subsequence
4MPQ_1,3NSP_1 150 4
4MPQ_1,1WFS_1 176 3
3NSP_1,1WFS_1 162 3

Newick tree

 
[
	1WFS_1:87.53,
	[
		4MPQ_1:75,3NSP_1:75
	]:12.53
]

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 \((0.85)(0.8)(\frac{569 }{\log_{20} 569}-\frac{240}{\log_{20}240})=93.5\)
Status Protein1 Protein2 d d1/2
Query variables 4MPQ_1 3NSP_1 119 101.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]