CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
6XPR_1 3NJY_1 4PII_1 Letter Amino acid
14 16 10 D Aspartic acid
17 23 10 T Threonine
2 12 8 M Methionine
13 23 12 F Phenylalanine
28 24 15 S Serine
14 23 11 A Alanine
25 15 7 N Asparagine
8 5 0 C Cysteine
9 31 21 E Glutamic acid
15 27 23 K Lycine
18 21 11 P Proline
5 8 7 W Tryptophan
11 21 9 Y Tyrosine
13 11 6 Q Glutamine
19 23 16 G Glycine
4 15 8 H Histidine
22 27 29 L Leucine
14 17 11 V Valine
16 19 15 R Arginine
24 20 21 I Isoleucine 

6XPR_1|Chains A, D|Hemagglutinin|Influenza A virus (A/Texas/50/2012(H3N2)) (1321009)
>3NJY_1|Chains A, B|Lysine-specific demethylase 4A|Homo sapiens (9606)
>4PII_1|Chain A|N-glycosylase/DNA lyase|Pyrococcus furiosus (186497)
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 \(w=f(c)\)
6XPR , Knot 129 291 0.83 40 195 284 
TNATELVQNSSIGEICDSPHQILDGENCTLIDALLGDPQCDGFQNKKWDLFVERSKAYSNCYPYDVPDYASLRSLVASSGTLEFNNESFNWNGVTQNGTSSACIRRSNNSFFSRLNWLTHLNFKYPALNVTMPNNEQFDKLYIWGVHHPVTDKDQIFLYAQPSGRITVSTKRSQQAVIPNIGFRPRIRNIPSRISIYWTIVKPGDILLINSTGNLIAPRGYFKIRSGKSSIMRSDAPIGKCKSECITPNGSIPNDKPFQNVNRITYGACPRYVKQSTLKLATGGALEVLFQ
3NJY , Knot 167 381 0.86 40 238 367 
MHHHHHHSSGVDLGTENLYFQSMASESETLNPSARIMTFYPTMEEFRNFSRYIAYIESQGAHRAGLAKVVPPKEWKPRASYDDIDDLVIPAPIQQLVTGQSGLFTQYNIQKKAMTVREFRKIANSDKYCTPRYSEFEELERKYWKNLTFNPPIYGADVNGTLYEKHVDEWNIGRLRTILDLVEKESGITIEGVNTPYLYFGMWKTSFAWHTEDMDLYSINYLHFGEPKSWYSVPPEHGKRLERLAKGFFPGSAQSCEAFLRHKMTLISPLMLKKYGIPFDKVTQEAGEFMITFPYGYHAGFNHGFNCAESTNFATRRWIEYGKQAVLCSCRKDMVKISMDVFVRKFQPERYKLWKAGKDNTVIDHTLPTPEAAEFLKESEL
4PII , Knot 111 250 0.81 38 164 240 
AHHHHHHGSRELVEIIKGIGIEGAKEVEEKVDRQFYALQYLFRHQDPEMFIKLVIANSLVSYQLTGRGEDWWWEFARYFSGREVDSIWKAYGEFLPKSKNNRRLIEAKLNRIRKVEGFLSTLTLKDLEGYYKNMKMLWKALIKIMGSREDSKTIVFTVKMFGYASRIAFSRFIPYPMEIPIPEDLRIKSVTSKLTQEKPTKFWMKIGQESGVPPLHIDSLIWPLLGNADLTPLDIELRNKLMKLTELLGL

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 \(c\).

\(|P_{f(6XPR_1)}(2) \setminus P_{f(3NJY_1)}(2)|=71\), \(|P_{f(3NJY_1)}(2) \setminus P_{f(6XPR_1)}(2)|=114\). 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 1:001001100001101000100110100001101111010001100001011100001000001001100101001110010101000010101100010001010000001100101100101001110101100001001011110011000001110101010101000000011110111010100110010101011011011110001011110101010010001100011110000001010101100011001001001101001000010110111101110
Pair \(Z_2\) Length of longest common subsequence
6XPR_1,3NJY_1 185 3
6XPR_1,4PII_1 181 3
3NJY_1,4PII_1 166 6

Newick tree

 
[
	6XPR_1:94.17,
	[
		4PII_1:83,3NJY_1:83
	]:11.17
]

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 \((0.85)(0.8)(\frac{672 }{\log_{20} 672}-\frac{291}{\log_{20}291})=105.\)
Status Protein1 Protein2 d d1/2
Query variables 6XPR_1 3NJY_1 141 121.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]