CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
3NFE_1 1ONX_1 5XXQ_1 Letter Amino acid
5 10 26 H Histidine
14 40 34 L Leucine
14 15 23 K Lycine
4 6 8 M Methionine
5 11 16 F Phenylalanine
5 26 23 T Threonine
2 1 13 W Tryptophan
1 6 5 C Cysteine
2 9 15 Q Glutamine
5 21 36 E Glutamic acid
10 27 25 I Isoleucine
14 25 42 S Serine
4 7 12 Y Tyrosine
4 12 23 N Asparagine
11 35 27 V Valine
13 37 26 A Alanine
5 16 11 R Arginine
9 25 38 D Aspartic acid
8 40 28 G Glycine
7 21 25 P Proline 

3NFE_1|Chains A, C|Hemoglobin subunit alpha-1|Trematomus newnesi (35730)
>1ONX_1|Chains A, B|Isoaspartyl dipeptidase|Escherichia coli (562)
>5XXQ_1|Chains A, B|Histone-binding protein RBBP4|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 \(w=f(c)\)
3NFE , Knot 72 143 0.83 42 115 138 
XSLSDKDKAAVRALWSKIGKSSDAIGNDALSRMIVVYPQTKIYFSHWPDVTPGSPNIKAHGKKVMGGIALAVSKIDDLKTGLMELSEQHAYKLRVDPSNFKILNHCILVVISTMFPKEFTPEAHVSLDKFLSGVALALAERYR
1ONX , Knot 160 390 0.81 40 202 365 
MIDYTAAGFTLLQGAHLYAPEDRGICDVLVANGKIIAVASNIPSDIVPNCTVVDLSGQILCPGFIDQHVHLIGGGGEAGPTTRTPEVALSRLTEAGVTSVVGLLGTDSISRHPESLLAKTRALNEEGISAWMLTGAYHVPSRTITGSVEKDVAIIDRVIGVKCAISDHRSAAPDVYHLANMAAESRVGGLLGGKPGVTVFHMGDSKKALQPIYDLLENCDVPISKLLPTHVNRNVPLFEQALEFARKGGTIDITSSIDEPVAPAEGIARAVQAGIPLARVTLSSDGNGSQPFFDDEGNLTHIGVAGFETLLETVQVLVKDYDFSISDALRPLTSSVAGFLNLTGKGEILPGNDADLLVMTPELRIEQVYARGKLMVKDGKACVKGTFETA
5XXQ , Knot 186 456 0.83 40 240 421 
MSYYHHHHHHDYDIPTTENLYFQGAMGSGIQMADKEAAFDDAVEERVINEEYKIWKKNTPFLYDLVMTHALEWPSLTAQWLPDVTRPEGKDFSIHRLVLGTHTSDEQNHLVIASVQLPNDDAQFDASHYDSEKGEFGGFGSVSGKIEIEIKINHEGEVNRARYMPQNPCIIATKTPSSDVLVFDYTKHPSKPDPSGECNPDLRLRGHQKEGYGLSWNPNLSGHLLSASDDHTICLWDISAVPKEGKVVDAKTIFTGHTAVVEDVSWHLLHESLFGSVADDQKLMIWDTRSNNTSKPSHSVDAHTAEVNCLSFNPYSEFILATGSADKTVALWDLRNLKLKLHSFESHKDEIFQVQWSPHNETILASSGTDRRLNVWDLSKIGEEQSPEDAEDGPPELLFIHGGHTAKISDFSWNPNEPWVICSVSEDNIMQVWQMAENIYNDEDPEGSVDPEGQGS

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 \(c\).

\(|P_{f(3NFE_1)}(2) \setminus P_{f(1ONX_1)}(2)|=42\), \(|P_{f(1ONX_1)}(2) \setminus P_{f(3NFE_1)}(2)|=129\). 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 1:00100000111011100110000111001100111101000101001101011010101010011111111100100100111010000100101010010110001111100111001010101010011011111110000
Pair \(Z_2\) Length of longest common subsequence
3NFE_1,1ONX_1 171 4
3NFE_1,5XXQ_1 185 4
1ONX_1,5XXQ_1 150 4

Newick tree

 
[
	3NFE_1:93.28,
	[
		1ONX_1:75,5XXQ_1:75
	]:18.28
]

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 \((0.85)(0.8)(\frac{533 }{\log_{20} 533}-\frac{143}{\log_{20}143})=114.\)
Status Protein1 Protein2 d d1/2
Query variables 3NFE_1 1ONX_1 142 96.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]