Alignment-free sequence analysis and applications
Genome and metagenome comparisons based on large amounts of next-generation
sequencing (NGS) data pose significant challenges for alignment-based approaches due to …
sequencing (NGS) data pose significant challenges for alignment-based approaches due to …
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 …
Survey of protocol reverse engineering algorithms: Decomposition of tools for static traffic analysis
Knowledge about a network protocol to understand the communication between entities is
necessary for vulnerability research, penetration testing, malware analysis, network …
necessary for vulnerability research, penetration testing, malware analysis, network …
Interpretable genotype-to-phenotype classifiers with performance guarantees
Understanding the relationship between the genome of a cell and its phenotype is a central
problem in precision medicine. Nonetheless, genotype-to-phenotype prediction comes with …
problem in precision medicine. Nonetheless, genotype-to-phenotype prediction comes with …
Predictive computational phenotyping and biomarker discovery using reference-free genome comparisons
Background The identification of genomic biomarkers is a key step towards improving
diagnostic tests and therapies. We present a reference-free method for this task that relies …
diagnostic tests and therapies. We present a reference-free method for this task that relies …
HAlign: Fast multiple similar DNA/RNA sequence alignment based on the centre star strategy
Motivation: Multiple sequence alignment (MSA) is important work, but bottlenecks arise in
the massive MSA of homologous DNA or genome sequences. Most of the available state-of …
the massive MSA of homologous DNA or genome sequences. Most of the available state-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 …
Beyond DNA barcoding: The unrealized potential of genome skim data in sample identification
Genetic tools are increasingly used to identify and discriminate between species. One key
transition in this process was the recognition of the potential of the ca 658bp fragment of the …
transition in this process was the recognition of the potential of the ca 658bp fragment of the …
kmacs: the k -mismatch average common substring approach to alignment-free sequence comparison
CA Leimeister, B Morgenstern - Bioinformatics, 2014 - academic.oup.com
Motivation: Alignment-based methods for sequence analysis have various limitations if large
datasets are to be analysed. Therefore, alignment-free approaches have become popular in …
datasets are to be analysed. Therefore, alignment-free approaches have become popular in …
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 …