e-journal

Thermodynamic Post-Processing versus GC-Content Pre-Processing for DNA Codes Satisfying the Hamming Distance and Reverse-Complement Constraints

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Stochastic, meta-heuristic and linear construction algorithms for the design of DNA strands satisfying Hamming distance and reverse-complement constraints often use a GC-content constraint to pre-process the DNA strands. Since GC-content is a poor predictor of DNA strand hybridization strength the strands can be filtered by post-processing using thermodynamic calculations. An alternative approach is considered here, where the algorithms are modified to remove consideration of GC-content and rely on postprocessing
alone to obtain large sets of DNA strands with satisfactory melting temperatures. The two approaches (pre-processing GC-content and post-processingmelting temperatures) are compared and are shown to be complementary when large DNA sets are desired. In particular, the second approach can give significant improvements when linear constructions are used.
Index Terms—DNA design, linear codes, stochastic local search, Hamming distance, reverse-complement

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Informasi Detail

Judul Seri

IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS

No. Panggil

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Penerbit

New York : IEEE., 2014

Deskripsi Fisik

IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS, VOL. 11, NO. 2, MARCH/APRIL 2014

Bahasa

English

ISBN/ISSN

1545-5963

Klasifikasi

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Tipe Isi

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Tipe Media

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Tipe Pembawa

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Edisi

VOL. 11, NO. 2, MARCH/APRIL 2014

Subjek

BIOLOGI

Info Detail Spesifik

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Pernyataan Tanggungjawab

Yuli/Agus

Versi lain/terkait

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