For any two q-ary sequences x and y, the stem similarity between them is defined as a total number of stems (blocks of length 2 consisting of adjacent elements of x and y) in their longest common Hamming subsequence. For q = 4 this similarity function and the corresponding distance function arise in molecular biology in describing an additive mathematical model of thermodynamic distance between DNA sequences. In the present paper, we derive explicit formulas for sphere sizes in this metric and consider their asymptotics in the case of spheres of a constant radius. Based on these results, we also obtain a random coding bound and Hamming bound for the optimal size of the so-called DNA codes for the case of a constant distance.
Problems of Information Transmission – Springer Journals
Published: Apr 23, 2010
It’s your single place to instantly
discover and read the research
that matters to you.
Enjoy affordable access to
over 18 million articles from more than
15,000 peer-reviewed journals.
All for just $49/month
Query the DeepDyve database, plus search all of PubMed and Google Scholar seamlessly
Save any article or search result from DeepDyve, PubMed, and Google Scholar... all in one place.
All the latest content is available, no embargo periods.
“Whoa! It’s like Spotify but for academic articles.”@Phil_Robichaud