CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
2RAX_1 8RMS_1 2VVH_1 Letter Amino acid
10 36 12 F Phenylalanine
5 49 9 S Serine
3 12 2 W Tryptophan
4 43 10 R Arginine
3 18 4 Q Glutamine
12 52 19 K Lycine
6 39 12 T Threonine
5 32 11 N Asparagine
6 37 17 D Aspartic acid
5 13 13 H Histidine
10 63 15 L Leucine
2 24 8 M Methionine
0 19 11 Y Tyrosine
15 78 14 E Glutamic acid
7 35 21 G Glycine
4 49 11 I Isoleucine
1 31 13 V Valine
9 36 12 A Alanine
6 17 3 C Cysteine
10 33 11 P Proline 

2RAX_1|Chains A, C[auth E], E[auth X]|Baculoviral IAP repeat-containing protein 5|Homo sapiens (9606)
>8RMS_1|Chain A|Polymerase acidic protein|Influenza A virus (A/Zhejiang/DTID-ZJU01/2013(H7N9)) (1318616)
>2VVH_1|Chains A, B, C, D|Green to red photoconvertible GFP-like protein EosFP|Lobophyllia hemprichii (46758)
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 \(w=f(c)\)
2RAX , Knot 62 123 0.80 38 98 116 
GSHMGAPTLPPAWQPFLKDHRISTFKNWPFLEGCACTPERMAEAGFIHCPTENEPDLAQCFFCFKELEGWEPDDDPIEEHKKHSSGCAFLSVKKQFEELTLGEFLKLDRERAKNKIAKETNNK
8RMS , Knot 280 716 0.85 40 298 662 
MEDFVRQCFNPMIVELAEKAMKEYGEDPKIETNKFASICTHLEVCFMYSDFHFIDERGESTIIESGDPNVLLKHRFEIIEGRDRTMAWTVVNSICNTTGVEKPKFLPDLYDYKENRFIEIGVTRREVHIYYLEKANKIKSEKTHIHIFSFTGEEMATKADYTLDEESRARIKTRLFTIRQEMASRGLWDSFRQSERGEETIEERFEITGTMRRLADQSLPPNFSSLENFRAYVDGFEPNGCIEGKLSQMSKEVNARIEPFLRTTPRPLRLPDGPPCSQRSKFLLMDALKLSIEDPSHEGEGIPLYDAIKCMKTFFGWKEPNIIKPHEKGINPNYLLTWKQVLAELQDIKNEEKIPRTKNMKKTSQLKWALGENMAPEKVDFEDCKDVNDLKQYDSDEPEPRSLACWIQSEFNKACELTDSSWVELDEIGEDVAPIEHIASMRRNYFTAEVSHCRATEYIMKGVYINTALLNASCAAMDDFQLIPMISKCITKEGRRKTNLYGFIIKGRSHLRNDTDVVNFVSMEFSLTDPRLEPHKWEKYCVLEIGDMLLRTAVGQVSRPMFLYVRTNGTSKIKMKWGMEMRRCLLQSLQQIESMIEAESSVKEKDLTKEFFENKSETWPIGESPKGVEEGSIGKVCRTLLAKSVFNSLYASPQLEGFSAESRKLLLIVQALRDNLEPGTFDLEGLYEAIEECLINDPWVLLNASWFNSFLTHALR
2VVH , Knot 103 228 0.81 40 163 218 
HHMSAIKPDMKINLRMEGNVNGHHFVIDGDGTGKPFEGKQSMDLEVKEGGPLPFAFDILTTAFHYGNRVFAEYPDHIQDYFKQSFPKGYSWERSLTFEDGGICIARNDITMEGDTFYNKVRFHGVNFPANGPVMQKKTLKWEPSTEKMYVRDGVLTGDITMALLLEGNAHYRCDSRTTYKAKEKGVKLPGYHLVDHCIEILSHDKDYNKVKLYEHAVAHSGLPDNARR

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 \(c\).

\(|P_{f(2RAX_1)}(2) \setminus P_{f(8RMS_1)}(2)|=19\), \(|P_{f(8RMS_1)}(2) \setminus P_{f(2RAX_1)}(2)|=219\). 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 1:100111101111101110000100100111101010010011011110010000101100110100101101000110000000010111010001001011011010000100011000000
Pair \(Z_2\) Length of longest common subsequence
2RAX_1,8RMS_1 238 3
2RAX_1,2VVH_1 179 3
8RMS_1,2VVH_1 201 3

Newick tree

 
[
	8RMS_1:11.20,
	[
		2RAX_1:89.5,2VVH_1:89.5
	]:26.70
]

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 \((0.85)(0.8)(\frac{839 }{\log_{20} 839}-\frac{123}{\log_{20}123})=201.\)
Status Protein1 Protein2 d d1/2
Query variables 2RAX_1 8RMS_1 257 149.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]