Discrete optimization for TSP-like genome mapping problems by Mester D., Ronin D., et al.

By Mester D., Ronin D., et al.

Guided evolution approach set of rules for traditional TSP as a foundation for fixing the genetic/genomic TSP-like difficulties -- Multilocus genetic mapping -- Multilocus consensus genetic mapping : formula, version and algorithms -- TSP-like challenge in actual mapping (PMP)

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Let Wmax be the maximum of log Pr(ci, cj). 2) where 1{Pr(ci, cj) > Pr0} is indicator function equal to 1, if Pr(ci, cj) >Pr0, and equal to zero otherwise. , 2004). Solution of TSP is considered as NP-hard problem. , 2004). 4. Re-Sampling Verification of the Obtained Solution The quality of ordering of clones within the contig is characterized not only by the value of the chosen criterion, but also by its robustness to small uncertainty of band content of the clones, that can be referred to as contig stability.

Jackknife on the population dataset. 5. If i < 100 then goto 1. 6. Detect and remove marker(s) causing local map instability. 7. If a marker was deleted then goto 2. 5a demonstrates a part of the map for the simulated data that contains some unstable areas. 5b) with stable marker ordering. 5 A fragment of the jackknife-based grid table for the map build on simulated data. (a) Initial order with unstable neighborhoods; (b) Stabilization of the order after removing problematic markers (# 6, 7 and 8).

0. All experiments were produced on a processor Pentium-IV (2000 Mhz, RAM 1GB) and operation system Windows-2003XP. 0. 26 D. Mester, D. Ronin, M. Frenkely et al. 1. 85 Complication type, % MC I MD <5 5-15 >15 <5 5-15 >15 <5 10-30 >30 MC - misclassification, I - Interference, MD - Missing data. For a comparison of efficiency of the three algorithms (GLS, ES-MPM, and GES) on the multipoint genetic mapping problem, five classes of UWSP were simulated (with 50÷800 loci). 2. During the experiments, for each algorithm we registered the best (min), the worse (max), and the average (aver) CPU time to reach the optimal solution.

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