CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
1RBY_1 6LVS_1 4JLG_1 Letter Amino acid
8 16 9 R Arginine
9 22 14 D Aspartic acid
7 16 16 P Proline
2 14 6 M Methionine
9 12 11 N Asparagine
3 7 5 C Cysteine
8 28 6 Q Glutamine
11 11 15 H Histidine
19 39 16 L Leucine
14 38 20 S Serine
1 15 16 Y Tyrosine
21 23 16 A Alanine
14 36 24 E Glutamic acid
15 19 21 G Glycine
16 19 12 I Isoleucine
12 34 12 K Lycine
7 17 9 F Phenylalanine
10 19 14 T Threonine
2 4 3 W Tryptophan
21 21 19 V Valine 

1RBY_1|Chains A, B, C, D|PHOSPHORIBOSYLGLYCINAMIDE FORMYLTRANSFERASE|Homo sapiens (9606)
>6LVS_1|Chains A, B, C, D, E, F|Ubiquitin carboxyl-terminal hydrolase 14|Homo sapiens (9606)
>4JLG_1|Chains A, B|Histone-lysine N-methyltransferase SETD7|Homo sapiens (9606)
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 \(w=f(c)\)
1RBY , Knot 93 209 0.79 40 138 198 
ARVAVLISGTGSNLQALIDSTREPNSSAQIDIVISNKAAVAGLDKAERAGIPTRVINHKLYKNRVEFDSAIDLVLEEFSIDIVCLAGFMRILSGPFVQKWNGKMLNIHPSLLPSFKGSNAHEQALETGVTVTGCTVHFVAEDVDAGQIILQEAVPVKRGDTVATLSERVKLAEHKIFPAALQLVASGTVQLGENGKICWVKEEHHHHHH
6LVS , Knot 171 410 0.83 40 236 384 
HHHHHHSSGLVPRGSHMTEEQLASAMELPCGLTNLGNTSYMNATVQCIRSVPELKDALKRYAGALRASGEMASAQYITAALRDLFDSMDKTSSSIPPIILLQFLHMAFPQFAEKGEQGQYLQQDANECWIQMMRVLQQKLEAIEDDSSAATPSKKKSLIDQFFGVEFETTMKCTESEEEEVTKGKENQLQLSCFINQEVKYLFTGLKLRLQEEITKQSPTLQRNALYIKSSKISRLPAYLTIQMVRFFYKEKESVNAKVLKDVKFPLMLDMYELCTPELQEKMVSFRSKFKDLEDKKVNQQPNTSDKKSSPQKEVKYEPFSFADDIGSNNCGYYDLQAVLTHQGRSSSSGHYVSWVKRKQDEWIKFDDDKVSIVTPEDILRLSGGGDWHIAYVLLYGPRRVEIMEEESEQ
4JLG , Knot 122 264 0.86 40 183 255 
QYKDNIRHGVCWIYYPDGGSLVGEVNEDGEMTGEKIAYVYPDERTALYGKFIDGEMIEGKLATLMSTEEGRPHFELMPGNSVYHFDKSTSSCISTNALLPDPYESERVYVAESLISSAGEGLFSKVAVGPNTVMSFYNGVRITHQEVDSRDWALNGNTLSLDEETVIDVPEPYNHVSKYCASLGHKANHSFTPNCIYDMFVHPRFGPIKCIRTLRAVEADEELTVAYGYDHSPPGKSGPEAPEWYQVELKAFQATQQKHHHHHH

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 \(c\).

\(|P_{f(1RBY_1)}(2) \setminus P_{f(6LVS_1)}(2)|=41\), \(|P_{f(6LVS_1)}(2) \setminus P_{f(1RBY_1)}(2)|=139\). 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 1:10111110101001011100000100010101110001111110010011110011000100001010011011100101011011111011011110010101101010111010100100011001101010010111001011011100111100100110100010110001111110111010101100101011000000000
Pair \(Z_2\) Length of longest common subsequence
1RBY_1,6LVS_1 180 6
1RBY_1,4JLG_1 173 6
6LVS_1,4JLG_1 159 6

Newick tree

 
[
	1RBY_1:91.00,
	[
		4JLG_1:79.5,6LVS_1:79.5
	]:11.50
]

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 \((0.85)(0.8)(\frac{619 }{\log_{20} 619}-\frac{209}{\log_{20}209})=116.\)
Status Protein1 Protein2 d d1/2
Query variables 1RBY_1 6LVS_1 142 106.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]