Benchmarking of alignment-free sequence comparison methods
Background Alignment-free (AF) sequence comparison is attracting persistent interest driven
by data-intensive applications. Hence, many AF procedures have been proposed in recent …
by data-intensive applications. Hence, many AF procedures have been proposed in recent …
Evolution of biosequence search algorithms: a brief survey
G Kucherov - Bioinformatics, 2019 - academic.oup.com
Motivation Although modern high-throughput biomolecular technologies produce various
types of data, biosequence data remain at the core of bioinformatic analyses. However …
types of data, biosequence data remain at the core of bioinformatic analyses. However …
Fast alignment-free sequence comparison using spaced-word frequencies
Motivation: Alignment-free methods for sequence comparison are increasingly used for
genome analysis and phylogeny reconstruction; they circumvent various difficulties of …
genome analysis and phylogeny reconstruction; they circumvent various difficulties of …
Skmer: assembly-free and alignment-free sample identification using genome skims
The ability to inexpensively describe taxonomic diversity is critical in this era of rapid climate
and biodiversity changes. The recent genome-skimming approach extends current …
and biodiversity changes. The recent genome-skimming approach extends current …
Spaced seeds improve k-mer-based metagenomic classification
Motivation: Metagenomics is a powerful approach to study genetic content of environmental
samples, which has been strongly promoted by next-generation sequencing technologies …
samples, which has been strongly promoted by next-generation sequencing technologies …
Information theory in computational biology: where we stand today
P Chanda, E Costa, J Hu, S Sukumar, J Van Hemert… - Entropy, 2020 - mdpi.com
“A Mathematical Theory of Communication” was published in 1948 by Claude Shannon to
address the problems in the field of data compression and communication over (noisy) …
address the problems in the field of data compression and communication over (noisy) …
Fast and accurate phylogeny reconstruction using filtered spaced-word matches
CA Leimeister, S Sohrabi-Jahromi… - …, 2017 - academic.oup.com
Motivation Word-based or 'alignment-free'algorithms are increasingly used for phylogeny
reconstruction and genome comparison, since they are much faster than traditional …
reconstruction and genome comparison, since they are much faster than traditional …
The Statistics of k-mers from a Sequence Undergoing a Simple Mutation Process Without Spurious Matches
k-mer-based methods are widely used in bioinformatics, but there are many gaps in our
understanding of their statistical properties. Here, we consider the simple model where a …
understanding of their statistical properties. Here, we consider the simple model where a …
kWIP: The k-mer weighted inner product, a de novo estimator of genetic similarity
Modern genomics techniques generate overwhelming quantities of data. Extracting
population genetic variation demands computationally efficient methods to determine …
population genetic variation demands computationally efficient methods to determine …
The number of k-mer matches between two DNA sequences as a function of k and applications to estimate phylogenetic distances
S Röhling, A Linne, J Schellhorn, M Hosseini… - Plos one, 2020 - journals.plos.org
We study the number N k of length-k word matches between pairs of evolutionarily related
DNA sequences, as a function of k. We show that the Jukes-Cantor distance between two …
DNA sequences, as a function of k. We show that the Jukes-Cantor distance between two …