+ Site Statistics
+ Search Articles
+ Subscribe to Site Feeds
EurekaMag Most Shared ContentMost Shared
EurekaMag PDF Full Text ContentPDF Full Text
+ PDF Full Text
Request PDF Full TextRequest PDF Full Text
+ Follow Us
Follow on FacebookFollow on Facebook
Follow on TwitterFollow on Twitter
Follow on Google+Follow on Google+
Follow on LinkedInFollow on LinkedIn

+ Translate

The use of simulated annealing in chromosome reconstruction experiments based on binary scoring

Genetics 132(2): 591-601
The use of simulated annealing in chromosome reconstruction experiments based on binary scoring
We present a method of combinatorial optimization, simulated annealing, to order clones in a library with respect to their position along a chromosome. This ordering method relies on scoring each clone for the presence or absence of specific target sequences, thereby assigning a digital signature to each clone. Specifically, we consider the hybridization of oligonucleotide probes to a clone to constitute the signature. In that the degree of clonal overlap is reflected in the similarity of their signatures, it is possible to construct maps based on the minimization of the differences in signatures across a reconstructed chromosome. Our simulations show that with as few as 30 probes and a clonal density of 4.5 genome equivalents, it is possible to assemble a small eukaryotic chromosome into 33 contiguous blocks of clones (contigs). With higher clonal densities and more probes, this number can be reduced to less than 5 contigs per chromosome.

(PDF 0-2 workdays service: $29.90)

Accession: 002530597

PMID: 1427046

Related references

Porous media microstructure reconstruction using pixel-based and object-based simulated annealing. Congres Geologique International, Resumes 33, 2008

A pixel selection rule based on the number of different-phase neighbours for the simulated annealing reconstruction of sandstone microstructure. Journal of Microscopy 234(3): 262-268, 2009

Evaluation of the physical annealing strategy for simulated annealing: a function-based analysis in the landscape paradigm. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics 85(5 Pt 2): 056704-056704, 2012

Automated seed detection and three-dimensional reconstruction. II. Reconstruction of permanent prostate implants using simulated annealing. Medical Physics 28(11): 2272-2279, 2002

Optimum encoding of binary phase-only filters with a simulated annealing algorithm. Optics Letters 14(11): 545-547, 1989

Simulated annealing of binary holograms for the interconnection of single-mode structures. Applied Optics 31(8): 1059-1066, 1992

Simulated annealing algorithm for binary phase only filters in pattern classification. Applied Optics 29(8): 1203-1208, 1990

SPECT reconstruction by simulated annealing. Physics in Medicine and Biology 34(3): 259-281, 1989

Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions. Journal of Molecular Biology 268(1): 209-225, 1997

Using simulated annealing for 3D reconstruction of orthopedic fracture. Medical Physics 31(8): 2184-2191, 2004