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 …
Applied bioinformatics for the identification of regulatory elements
WW Wasserman, A Sandelin - Nature Reviews Genetics, 2004 - nature.com
The compilation of multiple metazoan genome sequences and the deluge of large-scale
expression data have combined to motivate the maturation of bioinformatics methods for the …
expression data have combined to motivate the maturation of bioinformatics methods for the …
Insights into land plant evolution garnered from the Marchantia polymorpha genome
The evolution of land flora transformed the terrestrial environment. Land plants evolved from
an ancestral charophycean alga from which they inherited developmental, biochemical, and …
an ancestral charophycean alga from which they inherited developmental, biochemical, and …
Progressive Cactus is a multiple-genome aligner for the thousand-genome era
New genome assemblies have been arriving at a rapidly increasing pace, thanks to
decreases in sequencing costs and improvements in third-generation sequencing …
decreases in sequencing costs and improvements in third-generation sequencing …
The Ensembl gene annotation system
The Ensembl gene annotation system has been used to annotate over 70 different
vertebrate species across a wide range of genome projects. Furthermore, it generates the …
vertebrate species across a wide range of genome projects. Furthermore, it generates the …
NONCODE 2016: an informative and valuable data source of long non-coding RNAs
Abstract NONCODE (http://www. bioinfo. org/noncode/) is an interactive database that aims
to present the most complete collection and annotation of non-coding RNAs, especially long …
to present the most complete collection and annotation of non-coding RNAs, especially long …
GenASM: A high-performance, low-power approximate string matching acceleration framework for genome sequence analysis
Genome sequence analysis has enabled significant advancements in medical and scientific
areas such as personalized medicine, outbreak tracing, and the understanding of evolution …
areas such as personalized medicine, outbreak tracing, and the understanding of evolution …
Genome sequence-based species delimitation with confidence intervals and improved distance functions
Background For the last 25 years species delimitation in prokaryotes (Archaea and Bacteria)
was to a large extent based on DNA-DNA hybridization (DDH), a tedious lab procedure …
was to a large extent based on DNA-DNA hybridization (DDH), a tedious lab procedure …
Ensembl comparative genomics resources
J Herrero, M Muffato, K Beal, S Fitzgerald, L Gordon… - Database, 2016 - academic.oup.com
Evolution provides the unifying framework with which to understand biology. The coherent
investigation of genic and genomic data often requires comparative genomics analyses …
investigation of genic and genomic data often requires comparative genomics analyses …
The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution
International Peach Genome Initiative, I Verde… - Nature …, 2013 - nature.com
Rosaceae is the most important fruit-producing clade, and its key commercially relevant
genera (Fragaria, Rosa, Rubus and Prunus) show broadly diverse growth habits, fruit types …
genera (Fragaria, Rosa, Rubus and Prunus) show broadly diverse growth habits, fruit types …