Paper Info
Title
Analysis and Classification of Constrained DNA Elements with N-gram Graphs and Genomic Signatures.
Abstract
Most common methods for inquiring genomic sequence composition, are based on the bag-of-words approach and thus largely ignore the original sequence structure or the relative positioning of its constituent oligonucleotides. We here present a novel methodology that takes into account both word representation and relative positioning at various lengths scales in the form of n-gram graphs (NGG). We implemented the NGG approach on short vertebrate and invertebrate constrained genomic sequences of various origins and predicted functionalities and were able to efficiently distinguish DNA sequences belonging to the same species (intra-species classification). As an alternative method, we also applied the Genomic Signatures (GS) approach to the same sequences. To our knowledge, this is the first time that GS are applied on short sequences, rather than whole genomes. Together, the presented results suggest that NGG is an efficient method for classifying sequences, originating from a given genome, according to their function.
Year
DOI
Venue
2014
10.1007/978-3-319-07953-0_18
ALGORITHMS FOR COMPUTATIONAL BIOLOGY
Keywords
Field
DocType
genomic sequence representation,n-gram graphs,conserved non-coding elements,CNEs,UCEs,ultraconserved elements,classification,genomic signatures
Genome,Graph,Word representation,Pattern recognition,Computer science,DNA,Oligonucleotide,n-gram,Artificial intelligence,DNA sequencing,Computational biology
Conference
Volume
ISSN
Citations 
8542
0302-9743
1
PageRank 
References 
Authors
0.40
10
6
Name
Order
Citations
PageRank
Dimitris Polychronopoulos1765.12
Anastasia Krithara218015.63
Christoforos Nikolaou352.49
Georgios Paliouras41510120.93
Yannis Almirantis5786.84
George Giannakopoulos630.77