CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
4HHV_1 2WTF_1 8QTF_1 Letter Amino acid
5 9 2 W Tryptophan
7 29 10 V Valine
4 15 2 C Cysteine
5 53 14 K Lycine
6 18 11 Y Tyrosine
4 28 29 A Alanine
3 22 7 F Phenylalanine
7 30 12 G Glycine
4 9 4 H Histidine
6 41 14 I Isoleucine
5 53 25 L Leucine
9 50 18 S Serine
5 17 7 Q Glutamine
8 30 26 E Glutamic acid
9 39 17 D Aspartic acid
0 10 7 M Methionine
4 18 4 P Proline
4 22 10 T Threonine
6 21 15 R Arginine
4 22 8 N Asparagine 

4HHV_1|Chains A, B|Collagen type IV alpha-3-binding protein|Homo sapiens (9606)
>2WTF_1|Chains A, B|DNA POLYMERASE ETA|SACCHAROMYCES CEREVISIAE (4932)
>8QTF_1|Chains A, B, C, D, E, F, G, H, I, J|14-3-3-like protein GF14 omega|Arabidopsis thaliana (3702)
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 \(w=f(c)\)
4HHV , Knot 57 105 0.84 38 93 102 
GEFSGPPVERCGVLSKWTNYIHGWQDRWVVLKNNALSYYKSEDETEYGCRGSICLSKAVITPHDFDECRFDISVNDSVWYLRAQDPDHRQQWIDAIEQHKTESGY
2WTF , Knot 216 536 0.84 40 262 505 
MASWSHPQFEKGASTSLYKKAGRMSKFTWKELIQLGSPSKAYESSLACIAHIDMNAFFAQVEQMRCGLSKEDPVVCVQWNSIIAVSYAARKYGISRMDTIQEALKKCSNLIPIHTAVFKKGEDFWQYHDGCGSWVQDPAKQISVEDHKVSLEPYRRESRKALKIFKSACDLVERASIDEVFLDLGRICFNMLMFDNEYELTGDLKLKDALSNIREAFIGGNYDINSHLPLIPEKIKSLKFEGDVFNPEGRDLITDWDDVILALGSQVCKGIRDSIKDILGYTTSCGLSSTKNVCKLASNYKKPDAQTIVKNDCLLDFLDCGKFEITSFWTLGGVLGKELIDVLDLPHENSIKHIRETWPDNAGQLKEFLDAKVKQSDYDRSTSNIDPLKTADLAEKLFKLSRGRYGLPLSSRPVVKSMMSNKNLRGKSCNSIVDCISWLEVFCAELTSRIQDLEQEYNKIVIPRTVSISLKTKSYEVYRKSGPVAYKGINFQSHELLKVGIKFVTDLDIKGKNKSYYPLTKLSMTITNFDIIDLQK
8QTF , Knot 108 242 0.81 40 159 234 
GAMASGREEFVYMAKLAEQAERYEEMVEFMEKVSAAVDGDELTVEERNLLSVAYKNVIGARRASWRIISSIEQKEESRGNDDHVTAIREYRSKIETELSGICDGILKLLDSRLIPAAASGDSKVFYLKMKGDYHRYLAEFKTGQERKDAAEHTLAAYKSAQDIANAELAPTHPIRLGLALNFSVFYYEILNSPDRACNLAKQAFDEAIAELDTLGEESYKDSTLIMQLLRDNLTLWTSDMQD

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 \(c\).

\(|P_{f(4HHV_1)}(2) \setminus P_{f(2WTF_1)}(2)|=25\), \(|P_{f(2WTF_1)}(2) \setminus P_{f(4HHV_1)}(2)|=194\). 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 1:101011110001110010001011000111100011000000000001001010100111010010000101010001101010010000011011000000010
Pair \(Z_2\) Length of longest common subsequence
4HHV_1,2WTF_1 219 3
4HHV_1,8QTF_1 158 3
2WTF_1,8QTF_1 163 4

Newick tree

 
[
	2WTF_1:10.69,
	[
		4HHV_1:79,8QTF_1:79
	]:22.69
]

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 \((0.85)(0.8)(\frac{641 }{\log_{20} 641}-\frac{105}{\log_{20}105})=156.\)
Status Protein1 Protein2 d d1/2
Query variables 4HHV_1 2WTF_1 199 117
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]