CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
2BOL_1 3RJA_1 6ZLN_1 Letter Amino acid
11 14 9 Q Glutamine
15 23 23 I Isoleucine
25 44 16 A Alanine
15 19 20 R Arginine
3 10 4 W Tryptophan
30 40 21 V Valine
21 30 23 D Aspartic acid
18 24 13 P Proline
22 32 34 L Leucine
6 26 13 Y Tyrosine
12 24 9 N Asparagine
1 3 9 C Cysteine
10 13 21 H Histidine
27 29 24 K Lycine
8 5 8 M Methionine
15 24 17 F Phenylalanine
21 26 20 S Serine
12 28 16 T Threonine
30 17 24 E Glutamic acid
12 42 15 G Glycine 

2BOL_1|Chains A, B|SMALL HEAT SHOCK PROTEIN|TAENIA SAGINATA (6206)
>3RJA_1|Chain A|Carbohydrate oxidase|Microdochium nivale (5520)
>6ZLN_1|Chain A|Dual specificity protein kinase CLK1|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 \(w=f(c)\)
2BOL , Knot 137 314 0.83 40 193 302 
MSIFPTRDSRDLSSRRRSLIDWEFPQMALVPLDQVFDWAERSRQSLHDDIVNMHRNLFSLEPFTAMDNAFESVMKEMSAIQPREFHPELEYTQPGELDFLKDAYEVGKDGRLHFKVYFNVKNFKAEEITIKADKNKLVVRAQKSVACGDAAMSESVGRSIPLPPSVDRNHIQATITTDDVLVIEAPVNEPNYKAIKLSPEKGLAIQPSEVQERQLAVKNKEGLEIVTAEDGSKKIHLELKVDPHFAPKDVKVWAKGNKVYVHGVTGKEEKTENASHSEHREFYKAFVTPEVVDASKTQAEIVDGLMVVEAPLFK
3RJA , Knot 192 473 0.83 40 237 448 
GAIEACLSAAGVPIDIPGTADYERDVEPFNIRLPYIPTAIAQTQTTAHIQSAVQCAKKLNLKVSAKSGGHSYASFGFGGENGHLMVQLDRMIDVISYNDKTGIAHVEPGARLGHLATVLNDKYGRAISHGTCPGVGISGHFAHGGFGFSSHMHGLAVDSVVGVTVVLADGRIVEASATENADLFWGIKGAGSNFGIVAVWKLATFPAPKVLTRFGVTLNWKNKTSALKGIEAVEDYARWVAPREVNFRIGDYGAGNPGIEGLYYGTPEQWRAAFQPLLDTLPAGYVVNPTTSLNWIESVLSYSNFDHVDFITPQPVENFYAKSLTLKSIKGDAVKNFVDYYFDVSNKVKDRFWFYQLDVHGGKNSQVTKVTNAETAYPHRDKLWLIQFYDRYDNNQTYPETSFKFLDGWVNSVTKALPKSDWGMYINYADPRMDRDYATKVYYGENLARLQKLKAKFDPTDRFYYPQAVRPVK
6ZLN , Knot 146 339 0.83 40 210 328 
SMHLICQSGDVLSARYEIVDTLGEGAFGKVVECIDHKAGGRHVAVKIVKNVDRYCEAARSEIQVLEHLNTTDPNSTFRCVQMLEWFEHHGHICIVFELLGLSTYDFIKENGFLPFRLDHIRKMAYQICKSVNFLHSNKLTHTDLKPENILFVQSDYTEAYNPKIKRDERTLINPDIKVVDFGSATYDDEHHSTLVSTRHYRAPEVILALGWSQPCDVWSIGCILIEYYLGFTVFPTHDSKEHLAMMERILGPLPKHMIQKTRKRKYFHHDRLDWDEHSSAGRYVSRACKPLKEFMLSQDVEHERLFDLIQKMLEYDPAKRITLREALKHPFFDLLKKSI

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 \(c\).

\(|P_{f(2BOL_1)}(2) \setminus P_{f(3RJA_1)}(2)|=51\), \(|P_{f(3RJA_1)}(2) \setminus P_{f(2BOL_1)}(2)|=95\). 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 1:10111000000100000011010110111111001101100000010001101000110101101100110011001011010010101000011010110010011001010101010100101001010100001110100011010111000110011111010000101010000111101110010001101010011110100100001110000110110100100010101010101110010111010010101101000000010000000100111010110100001011011111011110
Pair \(Z_2\) Length of longest common subsequence
2BOL_1,3RJA_1 146 4
2BOL_1,6ZLN_1 163 4
3RJA_1,6ZLN_1 171 3

Newick tree

 
[
	6ZLN_1:86.74,
	[
		2BOL_1:73,3RJA_1:73
	]:13.74
]

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 \((0.85)(0.8)(\frac{787 }{\log_{20} 787}-\frac{314}{\log_{20}314})=129.\)
Status Protein1 Protein2 d d1/2
Query variables 2BOL_1 3RJA_1 162 135.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]