CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
5DMV_1 1OLX_1 8YFT_1 Letter Amino acid
17 28 21 R Arginine
10 28 30 G Glycine
12 22 23 I Isoleucine
10 19 27 V Valine
14 36 36 A Alanine
13 17 40 N Asparagine
13 23 31 D Aspartic acid
15 27 48 E Glutamic acid
5 12 21 H Histidine
13 23 31 Y Tyrosine
3 4 22 W Tryptophan
6 5 8 C Cysteine
8 23 27 Q Glutamine
11 18 34 K Lycine
7 17 26 F Phenylalanine
7 21 29 P Proline
13 14 35 T Threonine
33 26 56 L Leucine
4 11 21 M Methionine
23 26 39 S Serine 

5DMV_1|Chain A[auth C]|Serine/threonine-protein kinase PLK1|Mus musculus (10090)
>1OLX_1|Chain A|2-OXOISOVALERATE DEHYDROGENASE ALPHA SUBUNIT|HOMO SAPIENS (9606)
>8YFT_1|Chain A|Angiotensin-converting enzyme|Nyctereutes procyonoides (34880)
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 \(w=f(c)\)
5DMV , Knot 111 237 0.85 40 163 230 
NEAIECHLSDLLQQLTSVNASKPSERGLVRQEEAEDPACIPIFWVSKWVDYSDKYGLGYQLCDNSVGVLFNDSTRLILYNDGDSLQYIERDGTESYLTVSSHPNSLMKKITLLNYFRNYMSEHLLKAGANITPREGDELARLPYLRTWFRTRSAIILHLSNGTVQINFFQDHTKLILCPLMAAVTYINEKRDFQTYRLSLLEEYGCCKELASRLRYARTMVDKLLSSRSASNRLKAS
1OLX , Knot 172 400 0.86 40 240 390 
SSLDDKPQFPGASAEFIDKLEFIQPNVISGIPIYRVMDRQGQIINPSEDPHLPKEKVLKLYKSMTLLNTMDRILYESQRQGRISFYMTNYGEEGTHVGSAAALDNTDLVFGQYREAGVLMYRDYPLELFMAQCYGNISDLGKGRQMPVHYGCKERHFVTISSPLATQIPQAVGAAYAAKRANANRVVICYFGEGAASEGDAHAGFNFAATLECPIIFFCRNNGYAISTPTSEQYRGDGIAARGPGYGIMSIRVDGNDVFAVYNATKEARRRAVAENQPFLIEAMTYRIGHHSTSDDSSAYRSVDEVNYWDKQDHPISRLRHYLLSQGWWDEEQEKAWRKQSRRKVMEAFEQAERKPKPNPNLLFSDVYQEMPAQLRKQQESLARHLQTYGEHYPLDHFDK
8YFT , Knot 244 605 0.86 40 296 574 
QSTEDLVNTFLEKFNYEAEELSYQSSLASWNYNTNITDENLQKMNNAGAKWSAFYEEQSKLAKTYPLEEIQDSTVKRQLRALQHSGSSVLSADKNQRLNTILNSMSTIYSTGKACNPSNPQECLLLEPGLDDIMENSKDYNERLWAWEGWRSEVGKQLRPLYEEYVALKNEMARANNYEDYGDYWRGDYEEEWENGYNYSRNQLIDDVEHTFTQIMPLYQHLHAYVRTKLMDTYPSYISPTGCLPAHLLGDMWGRFWTNLYPLTVPFGQKPNIDVTNAMVNQSWDARKIFKEAEKFFVSVGLPNMTQGFWENSMLTEPSDSWKVVCHPTAWDLGRGDFRIKMCTKVTMDDFLTAHHEMGHIQYDMAYAAQPFLLRNGANEGFHEAVGEIMSLSAATPNHLKNIGLLPPSFFEDSETEINFLLKQALTIVGTLPFTYMLEKWRWMVFKGEIPKDQWMKTWWEMKRNIVGVVEPVPHDETYCDPASLFHVANDYSFIRYYTRTIYQFQFQEALCQIAKHEGPLHKCDISNSSEAGQKLLEMLKLGKSKPWTYALEIVVGAKNMDVRPLLNYFEPLFTWLKEQNRNSFVGWNTDWSPYADQSHHHHHH

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 \(c\).

\(|P_{f(5DMV_1)}(2) \setminus P_{f(1OLX_1)}(2)|=43\), \(|P_{f(1OLX_1)}(2) \setminus P_{f(5DMV_1)}(2)|=120\). 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 1:001100010011001001010010001110000100110111111001100000011100100001111100000111000100100100010000101000100110010110010001000110111010100100110110100110000111101001010101100000111011111100100000100001011000100001100100100110011000010001010
Pair \(Z_2\) Length of longest common subsequence
5DMV_1,1OLX_1 163 4
5DMV_1,8YFT_1 185 5
1OLX_1,8YFT_1 152 4

Newick tree

 
[
	5DMV_1:90.59,
	[
		1OLX_1:76,8YFT_1:76
	]:14.59
]

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 \((0.85)(0.8)(\frac{637 }{\log_{20} 637}-\frac{237}{\log_{20}237})=112.\)
Status Protein1 Protein2 d d1/2
Query variables 5DMV_1 1OLX_1 146 113
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]