CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
5NFM_1 7DMP_1 7NRT_1 Letter Amino acid
4 25 14 R Arginine
9 45 49 G Glycine
5 29 15 I Isoleucine
4 10 6 M Methionine
3 59 43 P Proline
3 38 35 T Threonine
12 46 34 A Alanine
3 14 12 H Histidine
5 50 21 L Leucine
3 29 44 K Lycine
0 10 0 W Tryptophan
2 27 5 Y Tyrosine
5 35 27 V Valine
2 30 11 N Asparagine
0 6 2 C Cysteine
4 104 27 E Glutamic acid
5 39 29 D Aspartic acid
4 37 19 Q Glutamine
1 21 3 F Phenylalanine
1 62 45 S Serine 

5NFM_1|Chain A|YrbA|Sinorhizobium meliloti 2011 (1286640)
>7DMP_1|Chains A[auth B], B[auth b]|Radial spoke head protein 4 homolog A|Mus musculus (10090)
>7NRT_1|Chains A, B, C, D, E, F, G, H, I, J|Microtubule-associated protein tau|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 \(w=f(c)\)
5NFM , Knot 42 75 0.80 36 63 73 
MAPGDIEDMIKAGIPGARVTIRDLAGDGDHYAAEVVAEAFRGKTRVQQHQMVYNALKGNMGGILHALALQTSAPE
7DMP , Knot 271 716 0.83 40 278 632 
MENSTSLKQEKENQEPGEAERLWQGESDVSPQEPGPPSPEYREEEQRTDTEPAPRMSPSWSHQSRVSLSTGDLTAGPEVSSSPPPPPLQFHSTPLNTETTQDPVAASPTEKTANGIADTGTPYSDPWESSSAAKQSTSHYTSHAEESTFPQSQTPQPDLCGLRDASRNKSKHKGLRFDLLQEEGSDSNCDPDQPEVGASEAAQSMLEVAIQNAKAYLLSTSSKSGLNLYDHLSKVLTKILDERPADAVDIIENISQDVKMAHFNKKLDTLHNEYEMLPAYEIAETQKALFLQGHLEGADSELEEEMAESSLPNVMESAYYFEQAGVGLGTDETYRVFLALKQLTDTHPIQRCRFWGKILGLEMNYIVAEVEFRDGEDEEEVEEEGIAEERDNGGSEAGEEEEEELPKSLYKAPQVIPKEESRTGANKYVYFVCNVPGRPWVRLPSVTPAQIVTARKIKKFFTGRLDAAVISYPPFPGNESNYLRAQIARISAGTHVSPLGFYQFGEEEGEEEEVEGGRDSYEENPDFEGIQVIDLVESLSNWVHHVQYILPQGRCNWFNPIQKDEDEEEEEEEDEEKGEEPDYIEQEVGPPLLTPISEDLGIQNIPSWTTQLSSNLIPQYAIAVLRSNLWPGAYAFSNGKKFENFYIGWGHKYCVENYTPPSPPPVYQEYPSGPEITEMNDPSVEEEQAFRMTQEPVALSTEENEGTEDEDEDDED
7NRT , Knot 167 441 0.76 38 190 383 
MAEPRQEFEVMEDHAGTYGLGDRKDQGGYTMHQDQEGDTDAGLKESPLQTPTEDGSEEPGSETSDAKSTPTAEDVTAPLVDEGAPGKQAAAQPHTEIPEGTTAEEAGIGDTPSLEDEAAGHVTQARMVSKSKDGTGSDDKKAKGADGKTKIATPRGAAPPGQKGQANATRIPAKTPPAPKTPPSSGEPPKSGDRSGYSSPGSPGTPGSRSRTPSLPTPPTREPKKVAVVRTPPKSPSSAKSRLQTAPVPMPDLKNVKSKIGSTENLKHQPGGGKVQIINKKLDLSNVQSKCGSKDNIKHVPGGGSVQIVYKPVDLSKVTSKCGSLGNIHHKPGGGQVEVKSEKLDFKDRVQSKIGSLDNITHVPGGGNKKIETHKLTFRENAKAKTDHGAEIVYKSPVVSGDTSPRHLSNVSSTGSIDMVDSPQLATLADEVSASLAKQGL

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 \(c\).

\(|P_{f(5NFM_1)}(2) \setminus P_{f(7DMP_1)}(2)|=14\), \(|P_{f(7DMP_1)}(2) \setminus P_{f(5NFM_1)}(2)|=229\). 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 1:111101001101111110101001110100011011101101000100001100110101111101111000110
Pair \(Z_2\) Length of longest common subsequence
5NFM_1,7DMP_1 243 3
5NFM_1,7NRT_1 161 3
7DMP_1,7NRT_1 142 5

Newick tree

 
[
	5NFM_1:11.71,
	[
		7NRT_1:71,7DMP_1:71
	]:40.71
]

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 \((0.85)(0.8)(\frac{791 }{\log_{20} 791}-\frac{75}{\log_{20}75})=206.\)
Status Protein1 Protein2 d d1/2
Query variables 5NFM_1 7DMP_1 253 139
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]

Graphviz Engine:
Graphviz Engine: