Alignment-free sequence comparison: benefits, applications, and tools
Alignment-free sequence analyses have been applied to problems ranging from whole-
genome phylogeny to the classification of protein families, identification of horizontally …
genome phylogeny to the classification of protein families, identification of horizontally …
Genomic signatures of high-altitude adaptation and chromosomal polymorphism in geladas
Primates have adapted to numerous environments and lifestyles but very few species are
native to high elevations. Here we investigated high-altitude adaptations in the gelada …
native to high elevations. Here we investigated high-altitude adaptations in the gelada …
Alignment-based and alignment-free methods converge with experimental data on amino acids coded by stop codons at split between nuclear and mitochondrial …
H Seligmann - Biosystems, 2018 - Elsevier
Genetic codes mainly evolve by reassigning punctuation codons, starts and stops. Previous
analyses assuming that undefined amino acids translate stops showed greater divergence …
analyses assuming that undefined amino acids translate stops showed greater divergence …
A survey on data compression methods for biological sequences
The ever increasing growth of the production of high-throughput sequencing data poses a
serious challenge to the storage, processing and transmission of these data. As frequently …
serious challenge to the storage, processing and transmission of these data. As frequently …
The domestication of Cucurbita argyrosperma as revealed by the genome of its wild relative
J Barrera-Redondo, G Sanchez-de La Vega… - Horticulture …, 2021 - academic.oup.com
Despite their economic importance and well-characterized domestication syndrome, the
genomic impact of domestication and the identification of variants underlying the …
genomic impact of domestication and the identification of variants underlying the …
Efficient DNA sequence compression with neural networks
Background The increasing production of genomic data has led to an intensified need for
models that can cope efficiently with the lossless compression of DNA sequences. Important …
models that can cope efficiently with the lossless compression of DNA sequences. Important …
New insights into mammalian sex chromosome structure and evolution using high-quality sequences from bovine X and Y chromosomes
Background Mammalian X chromosomes are mainly euchromatic with a similar size and
structure among species whereas Y chromosomes are smaller, have undergone substantial …
structure among species whereas Y chromosomes are smaller, have undergone substantial …
K-mer Content, Correlation, and Position Analysis of Genome DNA Sequences for the Identification of Function and Evolutionary Features
A Sievers, K Bosiek, M Bisch, C Dreessen, J Riedel… - Genes, 2017 - mdpi.com
In genome analysis, k-mer-based comparison methods have become standard tools.
However, even though they are able to deliver reliable results, other algorithms seem to …
However, even though they are able to deliver reliable results, other algorithms seem to …
Functionality of Two Origins of Replication in Vibrio cholerae Strains With a Single Chromosome
Chromosomal inheritance in bacteria usually entails bidirectional replication of a single
chromosome from a single origin into two copies and subsequent partitioning of one copy …
chromosome from a single origin into two copies and subsequent partitioning of one copy …
Smash++: an alignment-free and memory-efficient tool to find genomic rearrangements
Background The development of high-throughput sequencing technologies and, as its
result, the production of huge volumes of genomic data, has accelerated biological and …
result, the production of huge volumes of genomic data, has accelerated biological and …