5.1 Contact Map
5.3.1 Algorithma Brand and Bound
(1) Batasan (Bounding)pencarian untuk memberikan sub masalah dari penyele-saian massalah suatu batas bawah masalah untuk penyelepenyele-saian yang terbaik nilai yang diproleh pada sub masalah;
(2) Suatu strategi untuk penyelesaian,penyelesaian yang benar dari sub masalah pada pencarian dari proses iterasi (peng,ulangan);
(3) Aturan pencabangan (Branching rule)di aplikasikan jika sub masalah setelah pencarian yang tidak dapat di buang ( dihilangkan)dengan ini dibagi dengan sub masalah yang sama kedalam dua a.tau lebih sub masalah untuk diselidiki sub barisan iterasi.
KESIMPULAN
Disertasi ini memberikan kontribusi pad.a masalah pemodelan <la.lam bidang biolo-gi molekulair untuk mendapatkan nilai optimal.Hasil model yang diproleh adalah dalam bentuk
m n m n m n
max
LL
WijXij+LL
WiiY(ij),(tk)+LL
WijCij+
(6.0.1)Kendala
i=l j=l i=l j=l i=l j=l
m n m n
LL LL
aijbjtXijXkt i=l j=l k=l l=lL
:Dz~\LnM\-1
Vlvf E A1lELnM
L
n Xij ~ 1, i = 1, 2, ... , m j=lm
L X i j ~ 1, j=l,2, ... ,n
i=l n
(6.0.2)
(6.0.:3)
(6.0.4)
L X k t
=
1, l=
1, 2, ... , m (6.0.5)l=l
L
m Xk/ ~ 1, k=
1, 2, ... , n (6.0.6)k=l
n m
LXk/ + LXkl
~ 1 (6.0.7)l=l k=1
Xij 2=". Yij,kl, i, k
=
1, 2, ... , m; j, l=
1, 2, ... , n (6.0.8)Xkt 2=". Yij,kl, i, k
=
1, 2, ... , m; j, l=
1, 2, ... , n (6.0.9)Xij
+
Xtk - Ytk,jl ~ 1 (6.0.10)XijE{0,1}, i=l,2, ... ,m; j=l,2, ... ,n
Xkt E {O, 1}, k
=
l, 2, ... , m; j=
1, 2, ... , n 52I 1111.II\ Pl.kti.:STAl< .. \AN I
___ Vf Pl,1TAS SUMATERA !ITARA.
j
Yij,kl E {0, l}, Yij,kl
=
{(i,j, k, l), (i, k) E E1; (i, l) E E2}Yij,kt(x)
= { ~:
untuk yang lainnya (i,j, k, l) E Y(x)53
dimana penambahan pad.a kendala baru, dua edges (v;,
vD
E E1 dan(v;, vt)
E E2 match (Yij,kl=
1) jika dan hanya jika. node pada dua edges menyajikan match, yaitu Xij=
1 dan Xkl=
1.Algorithma yang digunakan adalah Algorithma Lagrange dan Algorithma Brand and Bound.
Agarwal, P., dan Vishwamitra, L. (2011). Exhanced Matrix Model for Finding Se-quence Motif, IMS Engineering College, Radha Govind Engineering College Althaus E., Caprara A., Lenhof H-P dan Reiner K. (2006). A branch-and-cut algorithm for multiple sequence alignment, Math.Program., Ser. B 105,387-425.
Althaus E., Klau W G., Oliver K., Lenhof H-P., dan Reiner K. (2009). Integer Linear Programming in Computational Biology, LNCS 5760, pp.199-218.
Alterovitz G, dan Ramoni M F. (2007). Sistem Bioinformatics An Engineering Case-Based Approach, Artech House.
Andonov R., Yanev N dan Dognin M N.(2008). An Efficient Lagrange Relax-ation for the Contact Map Overlap Problem, WABI 2008(8th Workshop on Algorithms in Bioinformatics) 5251 (2008) 162-173 DOI:10.1007/978-3-540-8731-7-14
Bauer M, dan Klau G. W.(2004). Structural Alignment of Two RNA Sequence with Lagrangian Relaxation. Proc. Of ISAAC'04, LNCS, no. 3341, Springer, pp.131-123.
Bauer M., Klau G. W., dan Reinert K. (2007). An Exact Mathematical Pro-gramming Approach to Mv,ltiple RNA Sequence structure alignment, Freie Universitat Berlin.
Bauer M., Kla:u G. W., dan Reinert K.(2007). Accurate Multiple Sequence struc-ture ahgnrnent of RNA Sequence Using Combinatorial Optimization, Tech.
Report TR-B-07-06, Dept. of Mathematics and Computer Science, Free Uni-versity Berlin, Submittd to BMC Bioinformatics.
Bauer M., Klau G. W., dan Reinert K. (2005). Multiple structural RNA alignment with Lagrangian Relaxation, Proc. WABf '05 (R. Casadio dan G. Myers, eds.),LNBI, vol. 3692, pp. 303--314.
Caprara A. dan Lancia G.(2002). Structural Alignment of Large-Size Proteins via Lagrangian Relaxation, Proc. Of RECOMB'02, ACM Press, pp. 100-108.
Caprara A., Pisinger D dan Toth P.(1999). Exact Solution Quadratic Knapsack Problem, INFORMS J. on Computing 11 ,no. 2, 125-137
Czibula, G., Bocicor, M.I. dan Czibula, LG. (2011). An Experiment On Protein Structure Prediction Using Reinforcement Learning, Syudia Univ.Babes-Bolyai, Informatika, Volume LVI, Number 1
Dahl Geir.(1997). An introduction to convexity, polyhedral theory and combinato-rial optimization,University of Oslo Department of Informatics,.
Dahm R.(2005). Friedrich Miesher dan the discovery of DNA, Developmental Biology 278 (2005) 274-288
Daniele C., Ramamorthi R dan Russell S, A. (2013). Mi-red integer linear pro-gramming model to reconstuct phylogenies from single nucleotide polymor-phism haplotypes under the maximum parsimony criterion. Algorithms for Molecular Biology,83
54
55 Elzinga, C., Rahmann, S. clan Wang, H. (2007). Algorithm for Subsequence
Com-binatorics, University Amsterdam, Technical University of Dortmund, Uni-versity of Ulster,
Althaus E., Caprara A., Lehnof H-P, clan Reinert K. (2006). A Branch and cut algorithm for multiple sequence alignment, Math. Program.,Ser.B 105,387-425
Fisher L M,(2004). The Lagrangian Relaxation Method for Solving Integer Pro-gramming Problems, Management Science, Vol. 50,No.12, Ten Most Influen-tial Titles of Management Sciences First Fifty Years (Dec.,2004), pp.1861-1871
Florey G F (1979). Elementary Linear Algebra Aplications, Prentice-Hall, Inc., Englewood.
Forrester R J, Greenberg H J.(2008). Quadratic Binru·y Programming Model in Computation Biology, Algorithmic Operations Research Vol.3 (2008) 110-129
Greenberg J.H., Hart E.W dan Lancia G. (2004). Opportunities for Combinatorial Optimization in Computational Biology, INFORMS Journal on Computing, vol. 16, No. 3, Summer 2004, pp. 211-231.
Greenberg J.H.(2007). Integer Quadratic Programming Model in Computational Biology, Oprations Research Proceeding, Springer, Berlin, 2007,( Proceed-ings of German OR Society), 83-95.
Lehnof H-P., Reinert K., Mutzel P., Mehlhorn K., dan Kececioglu D J.(1999).
A Branch and c1.d algorithm for multiple sequence alignment.In:Proceedings of the First Annual International Conference on Computational Molecular Biology (RECOMB-97) 1999,pp241-249
Istrail S, dan Lam F. (2009). Combinatorial Algorithms for Protein Folding in Lat-tice Models : A Survey of Mathematical Result, International Press, Com-munications in Information and Sistems Vol.9 No.4,
Judson.WT (2009), Abstract Algebra Theory and Application, Stephen F.Austin State University.
Kellis M.(2012). Computional Biology: Genom, Network, Evolution MIT course 6.047 /6.878
Klug A.(2004). The Discovery of the DNA Double Helix, J. Mol. Biol 335, 3-26 Lancia G.(2004). Integer Programming Model for Computational Biology
Prob-lems, J. Comput. Sci. & Technol. Vol.19, No.1, pp.60-77
Laura G,Konstantions K,Adam N,dan Letchford. (2011). Gap inequalities for non-convex mixed-integer quadratic programs,Oprations Research Letters 39 (2011) 297-300
Lawler.LE (1976). Combinatorial Optimization: Networks and Matroids, Holt, Rinehart and Wiston.
Le Jon dan Leyffer Sven.(2012). Mixed Integer Nonlinear Programming, Springer Science+ Business Media,LLC.
Sven L., Linderoth, Luedtke, Miller Adan Todd M. (2009). Applications and Algo-rithms for Mixed Integer Nonlinear Programming, ARGONNE NATIONAL LABORATORY 9700 South Cass Avenue Argonne,Illionois
Duan L dan Sun X.(2006). NonLinear lntegerProgramming,Springer Sci-ence+ Business Media,LLC.
Needleman B.S dan Wunsch D.C.(1970). A General Method Applicable to the Search for Similarities in the Amino Acid Sequence of two Proteins, J. M ol.
Biol. 48,443-453.
Reidys C. (2011). Combinatorial Computational Biology of RNA, Pswdoknots and Neutral Networks,Springer Scienc+Business Media, LLC
Reinert Knut. (1999) A Polyhedral Approach to Sequence Alignment Prob-lems, PhD Dissertation.
Robert A, Stubbs, dan Sanjay M.(1999). A Branch and-cut method for 0-1 mixed convex programming, Math. Program., Ser. A 86:511-532.
Roger Q Y, Liu G.(2009). Graph Factors and Matching Extentions, Springer Dor-drecht Heidelberg London New York.
Rosenberg M S.(2009). Sequence Alignmen Methods, Models, Consepts, and Strategies, University of California Press.
Rush A.M. dan Collins M.(2012). A Tutorial on Dual Decomposition and La,.
grangian Relaxation for Inference in Natural Language Processing, .!011,rnal of Artificial Intelligence Research 45,305-362.
Samuel B., Adam N. dan Letchford. (2011). Unbounded Convex Set for nonconvex Mixed-Integer Quadratic Programming,working paper,Lancaster Universi-ty,Lancaster, UK.
Samuel B., Adam N, dan Letchford.(2012). Non-convex mixed-integer nonlinear programming: A survey, sttrvey in Operation Reseach and Management Sci-ence 17,97-106
Satya, R.V and Mekherjee, A., dan Ranga, U. (2003). A Pattern Matching Algo-rithm for Codon Optimization and CpG Motif Engineering in DNA Expres-sion Vectors, University Central Florida
Schrijver A. (2004). Combinatorial Optimization Polyhedra and Efficiency, Springer-Verlag Berlin Heidelberg.
Schrijver A. (1986). Theory of Linear and Integer Programming,John \Viley &
Sons Ltd.
Singla, N., dan Garg, D. (2012). String Matching Algorithms and Their Applica-bility in various Applications, Thappar University, International Jurnal of soft Computing and Engineering.
Sinha M.S. (2006). Mathematical Programming Theory and Methods,Reed Else-vier India Private Limited.
Smith, T.F. dan M.S. Waterman. (1981). Identification of common molecular sequence. J. Mol. Biol. 147, 38-46.
'
. JGLlKPlt-•• ~TAlU.AN l
~ S f l • :.·· · ,.fRAU1',.
j
•