Epitope prediction methods

Transcript

1 Downloaded from orbit.dtu.dk on: Oct 23, 2017 Epitope prediction methods Karosiene, Edita; Nielsen, Morten; Lund, Ole Publication date: 2013 Document Version Publisher's PDF, also known as Version of record Link back to DTU Orbit Citation (APA): Karosiene, E., Nielsen, M., & Lund, O. (2013). Epitope prediction methods. Kgs. Lyngby: Technical University of Denmark (DTU). General rights Copyright and moral rights for the publications made accessible in the public portal are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights. Users may download and print one copy of any publication from the public portal for the purpose of private study or research. You may not further distribute the material or use it for any profit-making activity or commercial gain You may freely distribute the URL identifying the publication in the public portal If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim.

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16 Chapter 1

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21 α β

22 O j o j = i H i w ij f (x) O j = f (o j ) f (x) = e x

23 Input layer I 1 I 2 I 3 I 4 I 5 Hidden layer H 1 H 2 H 3 H 4 H i w ij Output layer O 1 O j (i) (j) w ij

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25 n n n 1

26 '()*")(*" '+,-.-./")(*"!" &" &"!" %" $" #" %" $" #" '()*")(*" '+,-.-./")(*"

27 PCC = i (a i a)(p i p) i (a i a) 2 ( i (p i p) 2 a p a p a p 0

28 !" &" %" #" $" 23)4.4.5"/01" '()*+),-."/01" $" %" #"!" 23)4.4.5"/01" 6..03"%78-*9":3-//7()*49),-." 1/5 = TP AP = TN AN 1

29 !"#$%&'#$()*+,#(!"#$%&'( )'*+%&'( -&',*+()*+,#(!"#$%&'( )'*+%&'(!"# $%# $"#!%#

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31 !"#$%#&'()*+,!"!!#!$!"#$%"& '"'()"*&+,$#&!"! -.#/(/(0)*+,!"#$%"& '"'()"*&+,$#&!#%!"#$%"& '"'()"*&+,$#&!$! &"! -.+$/)& 0,$**.%1/2)1($3& 4, &#! -.+$/)& 0,$**.%1/2)1($3& 4, &$! -.+$/)& 0,$**.%1/2)1($3& 4, '(("% '((#% '(($% 6%1/714" 6%1/714" 6%1/714"!"!!#!$ )*+,-./0+%1+*23*456.+

32 Chapter 2

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43 N b N p < = N b < N p < { NetMHCpan Np < 50 N NetMHCcons = b < 10 NetMHC + NetMHCpan

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45 < { NetMHCpan D < 0.1 NetMHCcons = NetMHCpan + PickPocket D 0.1 NetMHC + NetMHCpan D = 0 NetMHCcons = NetMHCpan 0 < D < 0.1 NetMHCpan + PickPocket D 0.1 =

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50 Chapter 3

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56 α

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62 # # = =

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74 Chapter 4

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84 γ 22 6 = 132

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90 Chapter 5

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92 Capsid prm Envelope protein E NS1 NS2A NS2B NS3 NS4A NS4B NS5 protein C +

93 Epitope counts YF virus polyprotein sequence positions

94 YF-17D sequence NS NS2A +

95 < Epitope density C prm E NS1 NS2A NS2B NS3 NS4A NS4B NS5 Proteins

96 Number of epitopes !!!!!!!!! Protein length + <

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114 Appendix A

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130 Appendix B

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138 Appendix C

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