DNA codes for nonadditive stem similarity

DNA codes for nonadditive stem similarity DNA sequences are sequences with elements from the quaternary DNA alphabet {A, C, G, T}. An important property of them is their directedness and ability to form duplexes as a result of hybridization process, i.e., coalescing two oppositely directed sequences. In biological experiments exploiting this property it is necessary to generate an ensemble of such sequences (DNA codes) consisting of pairs of DNA sequences referred to as Watson-Crick duplexes. Furthermore, for any two words of the DNA code that do not form a Watson-Crick duplex, hybridization energy—stability measure of a potential DNA duplex—is upper bounded by a constant specified by conditions of an experiment. This problem can naturally be interpreted in terms of coding theory. Continuing our previous works, we consider a nonadditive similarity function for two DNA sequences, which most adequately models their hybridization energy. For the maximum cardinality of DNA codes based on this similarity, we establish a Singleton upper bound and present an example of an optimal construction. Using ensembles of DNA codes with special constraints on codewords, which we call Fibonacci ensembles, we obtain a random-coding lower bound on the maximum cardinality of DNA codes under this similarity function. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Problems of Information Transmission Springer Journals

DNA codes for nonadditive stem similarity

Loading next page...
 
/lp/springer_journal/dna-codes-for-nonadditive-stem-similarity-nYU0EIXAfp
Publisher
Pleiades Publishing
Copyright
Copyright © 2014 by Pleiades Publishing, Inc.
Subject
Engineering; Communications Engineering, Networks; Electrical Engineering; Information Storage and Retrieval; Systems Theory, Control
ISSN
0032-9460
eISSN
1608-3253
D.O.I.
10.1134/S0032946014030041
Publisher site
See Article on Publisher Site

Abstract

DNA sequences are sequences with elements from the quaternary DNA alphabet {A, C, G, T}. An important property of them is their directedness and ability to form duplexes as a result of hybridization process, i.e., coalescing two oppositely directed sequences. In biological experiments exploiting this property it is necessary to generate an ensemble of such sequences (DNA codes) consisting of pairs of DNA sequences referred to as Watson-Crick duplexes. Furthermore, for any two words of the DNA code that do not form a Watson-Crick duplex, hybridization energy—stability measure of a potential DNA duplex—is upper bounded by a constant specified by conditions of an experiment. This problem can naturally be interpreted in terms of coding theory. Continuing our previous works, we consider a nonadditive similarity function for two DNA sequences, which most adequately models their hybridization energy. For the maximum cardinality of DNA codes based on this similarity, we establish a Singleton upper bound and present an example of an optimal construction. Using ensembles of DNA codes with special constraints on codewords, which we call Fibonacci ensembles, we obtain a random-coding lower bound on the maximum cardinality of DNA codes under this similarity function.

Journal

Problems of Information TransmissionSpringer Journals

Published: Oct 16, 2014

References

You’re reading a free preview. Subscribe to read the entire article.


DeepDyve is your
personal research library

It’s your single place to instantly
discover and read the research
that matters to you.

Enjoy affordable access to
over 12 million articles from more than
10,000 peer-reviewed journals.

All for just $49/month

Explore the DeepDyve Library

Unlimited reading

Read as many articles as you need. Full articles with original layout, charts and figures. Read online, from anywhere.

Stay up to date

Keep up with your field with Personalized Recommendations and Follow Journals to get automatic updates.

Organize your research

It’s easy to organize your research with our built-in tools.

Your journals are on DeepDyve

Read from thousands of the leading scholarly journals from SpringerNature, Elsevier, Wiley-Blackwell, Oxford University Press and more.

All the latest content is available, no embargo periods.

See the journals in your area

DeepDyve Freelancer

DeepDyve Pro

Price
FREE
$49/month

$360/year
Save searches from
Google Scholar,
PubMed
Create lists to
organize your research
Export lists, citations
Read DeepDyve articles
Abstract access only
Unlimited access to over
18 million full-text articles
Print
20 pages/month
PDF Discount
20% off