CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
6QQE_1 7OPY_1 4YLB_1 Letter Amino acid
12 12 5 A Alanine
3 3 4 Q Glutamine
6 19 10 K Lycine
11 14 9 R Arginine
8 3 0 C Cysteine
3 15 2 F Phenylalanine
7 5 5 T Threonine
6 4 0 W Tryptophan
7 17 6 D Aspartic acid
2 16 13 E Glutamic acid
12 12 9 G Glycine
6 11 15 I Isoleucine
8 28 9 L Leucine
2 9 4 M Methionine
3 12 5 Y Tyrosine
14 8 5 N Asparagine
1 3 1 H Histidine
2 10 6 P Proline
10 11 7 S Serine
6 6 13 V Valine 

6QQE_1|Chain A|Lysozyme C|Gallus gallus (9031)
>7OPY_1|Chains A, B, C, D[auth F]|Glutathione transferase|Camelus dromedarius (9838)
>4YLB_1|Chains A, B, C, D|Heat shock protein Hsp20|Sulfolobus solfataricus (strain 98/2) (555311)
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 \(w=f(c)\)
6QQE , Knot 66 129 0.82 40 104 127 
KVFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDVQAWIRGCRL
7OPY , Knot 98 218 0.80 40 149 208 
MPMILGYWDIRGLAHAIRLLLEYTGSDYEEKIYSMGDAPDYDRSQWLSEKFKLGLDFPNLPYLIDGAHRLTQSNAILRYIARKHNLCGETEEEKIRVDVLENQAMDTRLDFARVCYNPDFEKLKPGFLKEIPEKMKLFSEFLGKRTWFAGDKLNYVDFLAYDVLDVYRIFEPKCLDEFPNLKDFMSRFEGLKKISAYMKSSRFLRSPLFLKMAMWGNK
4YLB , Knot 62 128 0.78 36 100 124 
GPGTMMNVIMREIGKKLDELSREFYESVIPPIDMYEEGGELVVVADLAGFNKDKISVRLSAQNELIINAEREIQYIGTKYATQRPLKIHKVIRLPVKVKRDSQVTDKYENGVLTIRIPVEGSVSIRIE

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 \(c\).

\(|P_{f(6QQE_1)}(2) \setminus P_{f(7OPY_1)}(2)|=63\), \(|P_{f(7OPY_1)}(2) \setminus P_{f(6QQE_1)}(2)|=108\). 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 1:011100011111000110000100110110110100010001000000100001110100011000100110001001100111000101010010011001011011111000001001011101001
Pair \(Z_2\) Length of longest common subsequence
6QQE_1,7OPY_1 171 3
6QQE_1,4YLB_1 148 2
7OPY_1,4YLB_1 167 3

Newick tree

 
[
	7OPY_1:87.72,
	[
		6QQE_1:74,4YLB_1:74
	]:13.72
]

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 \((0.85)(0.8)(\frac{347 }{\log_{20} 347}-\frac{129}{\log_{20}129})=66.7\)
Status Protein1 Protein2 d d1/2
Query variables 6QQE_1 7OPY_1 87 68
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]