CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
6ROW_1 3QMZ_1 3CXW_1 Letter Amino acid
10 36 7 W Tryptophan
42 79 7 Y Tyrosine
15 37 6 C Cysteine
52 291 38 L Leucine
12 49 13 H Histidine
20 56 4 M Methionine
41 140 14 F Phenylalanine
40 193 24 S Serine
43 128 8 N Asparagine
38 90 11 Q Glutamine
47 117 23 G Glycine
36 178 19 I Isoleucine
32 69 19 P Proline
42 144 8 T Threonine
41 102 21 R Arginine
46 143 20 D Aspartic acid
51 183 12 K Lycine
42 160 22 V Valine
53 103 14 A Alanine
52 188 24 E Glutamic acid 

6ROW_1|Chains A, B, C, D|Putative zinc metallopeptidase|Haemonchus contortus (6289)
>3QMZ_1|Chains A, B|Cytoplasmic dynein heavy chain|Saccharomyces cerevisiae (4932)
>3CXW_1|Chain A|Proto-oncogene serine/threonine-protein kinase Pim-1, Isoform 2|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 \(w=f(c)\)
6ROW , Knot 293 755 0.85 40 310 713 
NANRSKEWKNAANTLLFGLDESVDPCEDFYGFTCNKFIERIDLDELGRGRFTTFSQAQLEVNSDIVKALEKVDVNDEKFSQTERITKAAFQSCVEYTLKDDRKASVNELLQYISERFGGIPFLGQRVKGGCELYREMGRIEQQRALPTFMYTWVNVDHKNVSRNSYYISQPTLPMPREFYVLPQFAPELDARTKAIENVMKAFASDILKDPSKYDKMIKTAAREVTQIEQKIAMASWPDDELRNHEQQYNPYELFAPSEGKIALQDAFPNIRFGKYIAGLMETATGGVPVSPVFIGDVIVTNPAYMGFLNTLFRQTNIQMNQYPFVNYIIVHMLFEDAEHLGDKYLRIAKDADYVTYAQRKGVGITRSGRKYSRVFDERTDARMKCVDTITTYMPYGTGYVYVNSREDRDQVVEDVKQQTELIMKTFLKKMLSTLSWMQGESYRRAEKKINEMHRNYGWPKKLFGDFKNFDTIDAYHRDDYYSILEAYNNKTDKSTAFYTILNILRRGYENRESFRRKNETADRTNFLESPASVNAWYAPELNSLTLPFGILTSPHYDLQFPKAFNFAGSGTVGGHELVHGFDDEGVQFDYDGSLADCSVYECGWLEQKGKNGFKDMAQCVVTQYNAQCCPAKEGNVHCANGAHTQGENIADLGGLQASYNAYKEYIKMKGAEEMRLPGLEKFTPNQIFWISYGYSWCAKETQSSLVKRLLTNPHSPNSCRVNQVLQDIPSFAKDFQCALGQKMYPPAEQRCKVW
3QMZ , Knot 818 2486 0.85 40 371 1909 
EFVIEKSLNRIKKFWKEAQYEVIEHSSGLKLVREWDVLEQACKEDLEELVSMKASNYYKIFEQDCLDLESKLTKLSEIQVNWVEVQFYWLDLYGILGENLDIQNFLPLETSKFKSLTSEYKMITTRAFQLDTTIEVIHIPNFDTTLKLTIDSLKMIKSSLSTFLERQRRQFPRFYFLGNDDLLKIIGSGKHHDQVSKFMKKMFGSIESIIFFEDFITGVRSVEGEVLNLNEKIELKDSIQAQEWLNILDTEIKLSVFTQFRDCLGQLKDGTDIEVVVSKYIFQAILLSAQVMWTELVEKCLQTNEFSKYWKEVDMKIKGLLDKLNKSSDNVKKKIEALLVEYLHFNNVIGQLKNCSTKEEARLLWAKVQKFYQKNDTLDDLNSVFISQSGYLLQYKFEYIGIPERLIYTPLLLIGFATLTDSLHQKYGGCFFGPAGTGKTETVKAFGQNLGRVVVVFNCDDSFDYQVLSRLLVGITQIGAWGCFDEFNRLDEKVLSAVSANIQQIQNGLQVGKSHITLLEEETPLSPHTAVFITLNPGYNGRSELPENLKKSFREFSMKSPQSGTIAEMILQIMGFEDSKSLASKIVHFLELLSSKCSSMNHYHFGLRTLKGVLRNCSPLISEFGEGEKTVVESLKRVILPSLGDTDELVFKDELSKIFDSAGTPLNSKAIVQCLKDAGQRSGFSMSEEFLKKCMQFYYMQKTQQALILVGKAGCGKTATWKTVIDAMAIFDGHANVVYVIDTKVLTKESLYGSMLKATLEWRDGLFTSILRRVNDDITGTFKNSRIWVVFDSDLDPEYVEAMNSVLDDNKILTLPNGERLPIPPNFRILFETDNLDHTTPATITRCGLLWFSTDVCSISSKIDHLLNKSYEALDNKLSMFELDKLKDLISDSFDMASLTNIFTCSNDLVHILGVRTFNKLETAVQLAVHLISSYRQWFQNLDDKSLKDVITLLIKRSLLYALAGDSTGESQRAFIQTINTYFGHDSQELSDYSTIVIANDKLSFSSFCSEIPSVSLEAHEVMRPDIVIPTIDTIKHEKIFYDLLNSKRGIILCGPPGSGKTMIMNNALRNSSLYDVVGINFSKDTTTEHILSALHRHTNYVTTSKGLTLLPKSDIKNLVLFCDEINLPKLDKYGSQNVVLFLRQLMEKQGFWKTPENKWVTIERIHIVGACNPPTDPGRIPMSERFTRHAAILYLGYPSGKSLSQIYEIYYKAIFKLVPEFRSYTEPFARASVHLYNECKARYSTGLQSHYLFSPRELTRLVRGVYTAINTGPRQTLRSLIRLWAYEAWRIFADRLVGVKEKNSFEQLLYETVDKYLPNQDLGNISSTSLLFSGLLSLDFKEVNKTDLVNFIEERFKTFCDEELEVPMVIHESMVDHILRIDRALKQVQGHMMLIGASRTGKTILTRFVAWLNGLKIVQPKIHRHSNLSDFDMILKKAISDCSLKESRTCLIIDESNILETAFLERMNTLLANADIPDLFQGEEYDKLLNNLRNKTRSLGLLLDTEQELYDWFVGEIAKNLHVVFTICDPTNNKSSAMISSPALFNRCIINWMGDWDTKTMSQVANNMVDVVPMEFTDFIVPEVNKELVFTEPIQTIRDAVVNILIHFDRNFYQKMKVGVNPRSPGYFIDGLRALVKLVTAKYQDLQENQRFVNVGLEKLNESVLKVNELNKTLPKAPPEEKEASISLVKSLTFEKERWLNTTKQFSKTSQELIGNCIISSIYETYFGHLNERERGDMLVILKRLLGKFAVKYDVNYRFIDYLVTLDEKMKWLECGLDKNDYFLENMSIVMNSQDAVPFLLDPSSHMITVISNYYGNKTVLLSFLEEGFVKRLENAVRFGSVVIIQDGEFFDPIISRLISREFNHAGNRVTVEIGDHEVDVSGDFKLFIHSCDPSGDIPIFLRSRVRLVHFVTNKESIETRIFDITLTEENAEMQRKREDLIKLNTEYRLKLKNLEKRLLEELNNSQGNMLENDELMVTLNNLKKEAMNIEKKLSESEEFFPQFDNLVEEYSIIGKHSVKIFSMLEKFGQFHWFYGISIGQFLSCFKRVFIKKSRETRAARTRVDEILWLLYQEVYCQFSTALDKKFKMIMAMTMFCLYKFDIESEQYKEAVLTMIGVLSESSDGVPKLTVDTNDDLRYLWDYVTTKSYISALNWFKNEFFVDEWNIADVVANSENNYFTMASERDVDGTFKLIELAKASKESLKIIPLGSIENLNYAQEEISKSKIEGGWILLQNIQMSLSWVKTYLHKHVEETKAAEEHEKFKMFMTCHLTGDKLPAPLLQRTDRVVYEDIPGILDTVKDLWGSQFFTGKISGVWSVYCTFLLSWFHALITARTRLVPHGFSKKYYFNDCDFQFASVYLENVLATNSTNNIPWAQVRDHIATIVYGGKIDEEKDLEVVAKLCAHVFCGSDNLQIVPGVRIPQPLLQQSEEEERARLTAILSNTIEPADSLSSWLQLPRESILDYERLQAKEVASSTEQLLQEM
3CXW , Knot 136 314 0.83 40 196 297 
SMLLSKINSLAHLRAAPCNDLHATKLAPGKEKEPLESQYQVGPLLGSGGFGSVYSGIRVSDNLPVAIKHVEKDRISDWGELPNGTRVPMEVVLLKKVSSGFSGVIRLLDWFERPDSFVLILERPEPVQDLFDFITERGALQEELARSFFWQVLEAVRHCHNCGVLHRDIKDENILIDLNRGELKLIDFGSGALLKDTVYTDFDGTRVYSPPEWIRYHRYHGRSAAVWSLGILLYDMVCGDIPFEHDEEIIGGQVFFRQRVSSECQHLIRWCLALRPSDRPTFEEIQNHPWMQDVLLPQETAEIHLHSLSPGPSK

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 \(c\).

\(|P_{f(6ROW_1)}(2) \setminus P_{f(3QMZ_1)}(2)|=15\), \(|P_{f(3QMZ_1)}(2) \setminus P_{f(6ROW_1)}(2)|=76\). 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 1:01000001001100111110001010001011000011001010011010100100101010001101100101000010000010011100010001000001010011001000111111110010110010001101000011101100110100001000000100101111001011101110101000110011011100110010000011001100100100011110110001000000001001111001011100111010110011111001011111011111011100110111100110000101000111001110111001001100010110010010010001111000100000110000010100100100011010101010000000011001000001110011001100101101000001000100100001110011101001001010000000011010000000001100110110010000001000000100001100110101101101001011111100100010110110111010111001101100011010001011000100011100010011001100110000100011001010010110001001101111010001000010101100101111001010011110010010100000011001100100100001001100110110010011100101110000011
Pair \(Z_2\) Length of longest common subsequence
6ROW_1,3QMZ_1 91 4
6ROW_1,3CXW_1 196 3
3QMZ_1,3CXW_1 191 4

Newick tree

 
[
	3CXW_1:10.59,
	[
		6ROW_1:45.5,3QMZ_1:45.5
	]:63.09
]

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 \((0.85)(0.8)(\frac{3241 }{\log_{20} 3241}-\frac{755}{\log_{20}755})=584.\)
Status Protein1 Protein2 d d1/2
Query variables 6ROW_1 3QMZ_1 754 489
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]