CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
8XCW_1 4FRV_1 5SQM_1 Letter Amino acid
34 25 13 K Lycine
20 6 5 P Proline
20 8 2 R Arginine
24 16 9 D Aspartic acid
1 1 3 C Cysteine
37 23 13 G Glycine
5 3 6 H Histidine
29 10 6 I Isoleucine
12 4 11 S Serine
40 9 15 A Alanine
35 11 6 E Glutamic acid
39 19 22 V Valine
15 4 16 N Asparagine
10 2 3 Q Glutamine
24 7 19 L Leucine
14 4 2 M Methionine
16 4 7 Y Tyrosine
9 13 5 F Phenylalanine
23 14 6 T Threonine
12 2 0 W Tryptophan 

8XCW_1|Chain A|Glutamate dehydrogenase|Thermococcus profundus (49899)
>4FRV_1|Chain A|Peptidyl-prolyl cis-trans isomerase|Equus caballus (9796)
>5SQM_1|Chains A, B|Non-structural protein 3|Severe acute respiratory syndrome coronavirus 2 (2697049)
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 \(w=f(c)\)
8XCW , Knot 174 419 0.83 40 213 401 
MVEIDPFEMAVKQLERAAQYMDISEEALEWLKKPMRIVEVSVPIEMDDGSVKVFTGFRVQHNWARGPTKGGIRWHPAETLSTVKALATWMTWKVAVVDLPYGGGKGGIIVNPKELSEREQERLARAYIRAVYDVIGPWTDIPAPDVYTNPKIMGWMMDEYETIMRRKGPAFGVITGKPLSIGGSLGRGTATAQGAIFTIREAAKALGIDLKGKKIAVQGYGNAGYYTAKLAKEQLGMTVVAVSDSRGGIYNPDGLDPDEVLKWKREHGSVKDFPGATNITNEELLELEVDVLAPAAIEEVITEKNADNIKAKIVAEVANGPVTPEADDILREKGILQIPDFLCNAGGVTVSYFEWVQNINGYYWTEEEVREKLDKKMTKAFWEVYNTHKDKNIHMRDAAYVVAVSRVYQAMKDRGWVKK
4FRV , Knot 87 185 0.81 40 133 180 
AMDEKKKRPKVTVKVYFDLRIGDEDIGRVVIGLFGKTVPKTVDNFVALATGEKGFGYKDSKFHRVIKDFMIQGGDFTRGDGTGGKSIYGERFPDENFKLKHYGPGWVSMANAGKDTNGSQFFITTVKTAWLDGKHVVFGKVLEGMEVVRKVETTKTDGRDKPLKDVTIADCGKIEVEKPFAIAKE
5SQM , Knot 80 169 0.81 38 119 162 
SMVNSFSGYLKLTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGALNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFL

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 \(c\).

\(|P_{f(8XCW_1)}(2) \setminus P_{f(4FRV_1)}(2)|=118\), \(|P_{f(4FRV_1)}(2) \setminus P_{f(8XCW_1)}(2)|=38\). 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 1:11010110111001001100101000110110011011010111010010101101101000110110011101011001001011101101011110110111011111010010000000110101011001111100111101000101111110000011000111111101011011101101010101111010011011110101001110101011000101100011101111000011100101101001101000010100111100100001101010111111100110000100101011101101110101001100011101101100111101001011001010010000100010001001110100000000101001101111001001100011100
Pair \(Z_2\) Length of longest common subsequence
8XCW_1,4FRV_1 156 4
8XCW_1,5SQM_1 182 4
4FRV_1,5SQM_1 144 3

Newick tree

 
[
	8XCW_1:88.59,
	[
		4FRV_1:72,5SQM_1:72
	]:16.59
]

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 \((0.85)(0.8)(\frac{604 }{\log_{20} 604}-\frac{185}{\log_{20}185})=119.\)
Status Protein1 Protein2 d d1/2
Query variables 8XCW_1 4FRV_1 147 106
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]