Algorithms on strings, trees, and sequences: computer science and computational biology
Algorithms on strings, trees, and sequences: computer science and computational biology
Efficient reconstruction of sequences from their subsequences or supersequences
Journal of Combinatorial Theory Series A
Strand design for biomolecular computation
Theoretical Computer Science - Natural computing
A PCR-based Protocol for In Vitro Selection of Non-crosshybridizing Oligonucleotides
DNA8 Revised Papers from the 8th International Workshop on DNA Based Computers: DNA Computing
A Software Tool for Generating Non-crosshybridizing Libraries of DNA Oligonucleotides
DNA8 Revised Papers from the 8th International Workshop on DNA Based Computers: DNA Computing
IEEE Transactions on Information Theory
Problems of Information Transmission
On codeword design in metric DNA spaces
Natural Computing: an international journal
A multi-threaded DNA tag/anti-tag library generator for multi-core platforms
CIBCB'09 Proceedings of the 6th Annual IEEE conference on Computational Intelligence in Bioinformatics and Computational Biology
DNA codes based on stem similarities between DNA sequences
DNA13'07 Proceedings of the 13th international conference on DNA computing
Hardware acceleration for thermodynamic constrained DNA code generation
DNA13'07 Proceedings of the 13th international conference on DNA computing
Efficient algorithm for testing structure freeness of finite set of biomolecular sequences
DNA'05 Proceedings of the 11th international conference on DNA Computing
Designing nucleotide sequences for computation: a survey of constraints
DNA'05 Proceedings of the 11th international conference on DNA Computing
Reverse–complement similarity codes
General Theory of Information Transfer and Combinatorics
Hi-index | 0.00 |
Thermodynamic distance functions are important components in the construction of DNA codes and DNA codewords are structural and information building blocks in biomolecular computing and other biotechnical applications that employ DNA hybridization assays. We introduce new metrics for DNA code design that capture key aspects of the nearest neighbor thermodynamic model for hybridized DNA duplexes. One version of our metric gives the maximum number of stacked pairs of hydrogen bonded nucleotide base pairs that can be present in any secondary structure in a hybridized DNA duplex without pseudoknots. We introduce the concept of (t-gap) block isomorphic subsequences to describe new string metrics that are similar to the weighted Levenshtein insertion-deletion metric. We show how our new distances can be calculated by a generalization of the folklore longest common subsequence dynamic programming algorithm. We give a Varshamov-Gilbert like lower bound on the size of some of codes using our distance functions as constraints. We also discuss software implementation of our DNA code design methods.