CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
2FXE_1 5SFN_1 8IYI_1 Letter Amino acid
4 24 25 E Glutamic acid
13 16 16 G Glycine
15 21 19 I Isoleucine
0 24 20 S Serine
8 22 18 T Threonine
5 17 11 Q Glutamine
4 14 8 N Asparagine
3 14 8 R Arginine
1 13 10 H Histidine
9 36 23 L Leucine
8 18 22 K Lycine
6 14 14 P Proline
2 7 5 W Tryptophan
5 21 17 A Alanine
0 12 3 C Cysteine
2 12 7 M Methionine
2 15 11 F Phenylalanine
1 12 13 Y Tyrosine
7 16 25 V Valine
4 15 18 D Aspartic acid 

2FXE_1|Chains A, B|pol protein|Human immunodeficiency virus 1 (11676)
>5SFN_1|Chains A, B, C, D|cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A|Homo sapiens (9606)
>8IYI_1|Chains A, B|KLLA0B09372p|Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (284590)
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 \(w=f(c)\)
2FXE , Knot 52 99 0.80 36 78 95 
PQITLWKRPIVTVKIGGQLKEALLDTGADDTVIEEMNLPGKWKPKMIGGIGGFIKVRQYDQIIIEIAGHKAIGTVLVGPTPVNIIGRNLLTQIGATLNF
5SFN , Knot 152 343 0.86 40 221 334 
GSSICTSEEWQGLMQFTLPVRLCKEIELFHFDIGPFENMWPGIFVYMVHRSCGTSCFELEKLCRFIMSVKKNYRRVPYHNWKHAVTVAHCMYAILQNNHTLFTDLERKGLLIACLCHDLDHRGFSNSYLQKFDHPLAALYSTSTMEQHHFSQTVSILQLEGHNIFSTLSSSEYEQVLEIIRKAIIATDLALYFGNRKQLEEMYQTGSLNLNNQSHRDRVIGLMMTACDLCSVTKLWPVTKLTANDIYAEFWAEGDEMKKLGIQPIPMMDRDKKDEVPQGQLGFYNAVAIPCYTTLTQILPPTEPLLKACRDNLSQWEKVIRGEETATWISSPSVAQKAAASED
8IYI , Knot 133 293 0.86 40 192 282 
MSELTHPTIVDGWFREISDTMWPGQAMTLRVEKILHHEKSKYQDVLVFKSTDYGNVLVLDNAIQVTERDEFSYQEMIAHLALNSHPNPKKVLVIGGGDGGVLREIVKHDSVQEAWLCDIDEAVIRVSKEYLPEMAKSYSHPKVKTHIGDGFQFLRDYQNTFDVIITDSSDPEGPAASLFQQSYFELLNGALTEKGVISTQAESMWIHLPIIKELKKACKEVFPTVGYAYTTIPTYPTGQIGFMVCSKDANVDVTKPLRSISEEEEEAKYRYYNKKVHEASFVLPTWVAKELDL

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 \(c\).

\(|P_{f(2FXE_1)}(2) \setminus P_{f(5SFN_1)}(2)|=32\), \(|P_{f(5SFN_1)}(2) \setminus P_{f(2FXE_1)}(2)|=175\). 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 1:101011001110101110100111001100011001011101010111111111010000011101110011101111101101110011001110101
Pair \(Z_2\) Length of longest common subsequence
2FXE_1,5SFN_1 207 4
2FXE_1,8IYI_1 180 3
5SFN_1,8IYI_1 183 4

Newick tree

 
[
	5SFN_1:10.11,
	[
		2FXE_1:90,8IYI_1:90
	]:10.11
]

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 \((0.85)(0.8)(\frac{442 }{\log_{20} 442}-\frac{99}{\log_{20}99})=103.\)
Status Protein1 Protein2 d d1/2
Query variables 2FXE_1 5SFN_1 138 87.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]

Graphviz Engine:
Graphviz Engine: