CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
5HUN_1 7XYX_1 7LAT_1 Letter Amino acid
14 16 8 Q Glutamine
16 12 13 F Phenylalanine
20 9 9 P Proline
39 21 16 S Serine
35 17 20 V Valine
7 5 13 M Methionine
12 6 1 W Tryptophan
12 4 10 Y Tyrosine
26 9 11 R Arginine
17 10 16 N Asparagine
16 6 4 C Cysteine
17 18 24 E Glutamic acid
46 10 32 G Glycine
6 13 8 H Histidine
13 33 22 L Leucine
16 13 35 A Alanine
23 9 16 D Aspartic acid
25 16 33 I Isoleucine
15 9 23 K Lycine
25 14 16 T Threonine 

5HUN_1|Chain A|Neuraminidase|Influenza A virus (A/gyrfalcon/Washington/41088-6/2014(H5N8)) (1589663)
>7XYX_1|Chains A, B|Protein zyg-11 homolog B|Homo sapiens (9606)
>7LAT_1|Chain A|Ketol-acid reductoisomerase|Campylobacter jejuni (197)
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 \(w=f(c)\)
5HUN , Knot 172 400 0.86 40 229 384 
GSGDSGSPGGTYINNTEPICDVKGFAPFSKDNGIRVGSRGHIFVIREPFVSCSPVGCRTFFLTQGSLLNDKHSNGTVKDRSPFRTLMSVEVGQSPNVYQARFEAVAWSATACHDGKKWMAIGVTGPDSKAVAVVHYGGVPTDVVNSWAGDILRTQESSCTCIQGNCYWVMTDGPANRQAQYRIYKANQGKIIGRKDVSFSGGHIEECSCYPNDGKVECVCRDNWTGTNRPVLIISPDLSYRVGYLCAGLPSDTPRGEDTQFVGSCTSPMGNQGYGVKGFGFRQGTDVWVGRTISRTSRSGFEIIRIKNGWTQTSKEQIRRQVVVDNSNWSGYSGSFTLPVELSGRECLVPCFWVEMIRGRPEERTIWTSSSSIVMCGVDYEIADWSWHDGAILPFDIDKM
7XYX , Knot 115 250 0.84 40 164 240 
CFLHVGAQLGTELFIVRQLLQIVKQKTNQNSVDTTLKFTLSALWNLTDESPTTCRHFIENQGLELFMRVLESFPTESSIQQKVLGLLNNIAEVQELHSELMWKDFIDHISSLLHSVEVEVSYFAAGIIAHLISRGEQAWTLSRSQRNSLLDDLHSAILKWPTPECEMVAYRSFNPFFPLLGCFTTPGVQLWAVWAMQHVCSKNPSRYCSMLIEEGGLQHLYNIKDHEHTDPHVQQIAVAILDSLEKHIVR
7LAT , Knot 143 330 0.83 40 192 313 
MAITVYYDKDCDLNLIKSKKVAIIGFGSQGHAHAMNLRDNGVNVTIGLREGSVSAVKAKNAGFEVMSVSEASKIADVIMILAPDEIQADIFNVEIKPNLSEGKAIAFAHGFNIHYGQIVVPKGVDVIMIAPKAPGHTVRNEFTLGGGTPCLIAIHQDESKNAKNLALSYASAIGGGRTGIIETTFKAETETDLFGEQAVLCGGLSALIQAGFETLVEAGYEPEMAYFECLHEMKLIVDLIYQGGIADMRYSISNTAEYGDYITGPKIITEETKKAMKGVLKDIQNGVFAKDFILERRAGFARMHAERKNMNDSLIEKTGRNLRAMMPWIS

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 \(c\).

\(|P_{f(5HUN_1)}(2) \setminus P_{f(7XYX_1)}(2)|=133\), \(|P_{f(7XYX_1)}(2) \setminus P_{f(5HUN_1)}(2)|=68\). 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 1:1010010111001000011001011111000011011001011110011100011100011100101100000010100001100110101100101001010111101010001001111110110001111100111100110011101100000000010100011100111000100010010010111000101011010000001001010010000101000111110101000110101111000101000011100001110010110111100100111100100000011011010011000000010001110000101001010111010100011101110110101000011000001110110001101010011111101001
Pair \(Z_2\) Length of longest common subsequence
5HUN_1,7XYX_1 201 4
5HUN_1,7LAT_1 173 3
7XYX_1,7LAT_1 188 4

Newick tree

 
[
	7XYX_1:10.64,
	[
		5HUN_1:86.5,7LAT_1:86.5
	]:14.14
]

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 \((0.85)(0.8)(\frac{650 }{\log_{20} 650}-\frac{250}{\log_{20}250})=112.\)
Status Protein1 Protein2 d d1/2
Query variables 5HUN_1 7XYX_1 145 117
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]