CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
1JNJ_1 8ZJI_1 2OYF_1 Letter Amino acid
5 35 5 R Arginine
8 53 7 E Glutamic acid
3 25 11 G Glycine
7 80 9 L Leucine
5 32 4 F Phenylalanine
2 6 1 W Tryptophan
2 44 6 A Alanine
3 45 1 Q Glutamine
4 19 1 H Histidine
5 54 5 I Isoleucine
9 51 7 S Serine
6 18 9 Y Tyrosine
5 36 6 N Asparagine
2 13 14 C Cysteine
8 52 13 K Lycine
7 30 3 V Valine
7 47 7 D Aspartic acid
2 28 2 M Methionine
5 33 5 P Proline
5 32 5 T Threonine 

1JNJ_1|Chain A|beta2-microglobulin|Homo sapiens (9606)
>8ZJI_1|Chains A, D|Engulfment and cell motility protein 1|Homo sapiens (9606)
>2OYF_1|Chain A|Phospholipase A2 VRV-PL-VIIIa|Daboia russellii pulchella (97228)
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 \(w=f(c)\)
1JNJ , Knot 53 100 0.81 40 84 97 
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDWSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM
8ZJI , Knot 285 733 0.85 40 301 684 
GGSGGSMPPPADIVKVAIEWPGAYPKLMEIDQKKPLSAIIKEVCDGWSLANHEYFALQHADSSNFYITEKNRNEIKNGTILRLTTSPAQNAQQLHERIQSSSMDAKLEALKDLASLSRDVTFAQEFINLDGISLLTQMVESGTERYQKLQKIMKPCFGDMLSFTLTAFVELMDHGIVSWDTFSVAFIKKIASFVNKSAIDISILQRSLAILESMVLNSHDLYQKVAQEITIGQLIPHLQGSDQEIQTYTIAVINALFLKAPDERRQEMANILAQKQLRSIILTHVIRAQRAINNEMAHQLYVLQVLTFNLLEDRMMTKMDPQDQAQRDIIFELRRIAFDAESEPNNSSGSMEKRKSMYTRDYKKLGFINHVNPAMDFTQTPPGMLALDNMLYFAKHHQDAYIRIVLENSSREDKHECPFGRSSIELTKMLCEILKVGELPSETCNDFHPMFFTHDRSFEEFFCICIQLLNKTWKEMRATSEDFNKVMQVVKEQVMRALTTKPSSLDQFKSKLQNLSYTEILKIRQSERMNQEDFQSRPILELKEKIQPEILELIKQQRLNRLVEGTCFRKLNARRRQDKFWYCRLSPNHKVLHYGDLEESPQGEVPHDSLQDKLPVADIKAVVTGKDCPHMKEKGALKQNKEVLELAFSILYDSNCQLNFIAPDKHEYCIWTDGLNALLGKDMMSDLTRNDLDTLLSMEIKLRLLDLENIQIPDAPPPIPKEPSNYDFVYDCN
2OYF , Knot 60 121 0.79 40 95 118 
SLLEFGKMILEETGKLAIPSYSSYGCYCGWGGKGTPKDATDRCCFVHDCCYGNLPDCNPKSDRYKYKRVNGAIVCEKGTSCENRICECDKAAAICFRQNLNTYSKKYMLYPDFLCKGELKC

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 \(c\).

\(|P_{f(1JNJ_1)}(2) \setminus P_{f(8ZJI_1)}(2)|=17\), \(|P_{f(8ZJI_1)}(2) \setminus P_{f(1JNJ_1)}(2)|=234\). 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 1:1100010101000011001000110001011010010101100100100100001010001010110000101000000100100101001011010001
Pair \(Z_2\) Length of longest common subsequence
1JNJ_1,8ZJI_1 251 3
1JNJ_1,2OYF_1 127 3
8ZJI_1,2OYF_1 242 3

Newick tree

 
[
	8ZJI_1:13.53,
	[
		1JNJ_1:63.5,2OYF_1:63.5
	]:74.03
]

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 \((0.85)(0.8)(\frac{833 }{\log_{20} 833}-\frac{100}{\log_{20}100})=208.\)
Status Protein1 Protein2 d d1/2
Query variables 1JNJ_1 8ZJI_1 270 152
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]