Exact sequence variants should replace operational taxonomic units in marker-gene data analysis
Recent advances have made it possible to analyze high-throughput marker-gene
sequencing data without resorting to the customary construction of molecular operational�…
sequencing data without resorting to the customary construction of molecular operational�…
Powers and pitfalls in sequence analysis: the 70% hurdle
P Bork�- Genome research, 2000 - genome.cshlp.org
High-throughput technologies impress us almost every week with novel global results and
big numbers. They often reveal important general trends that are impossible to realize with�…
big numbers. They often reveal important general trends that are impossible to realize with�…
OMA standalone: orthology inference among public and custom genomes and transcriptomes
AM Altenhoff, J Levy, M Zarowiecki, B Tomiczek…�- Genome�…, 2019 - genome.cshlp.org
Genomes and transcriptomes are now typically sequenced by individual laboratories but
analyzing them often remains challenging. One essential step in many analyses lies in�…
analyzing them often remains challenging. One essential step in many analyses lies in�…
[HTML][HTML] Apollo: democratizing genome annotation
Genome annotation is the process of identifying the location and function of a genome's
encoded features. Improving the biological accuracy of annotation is a complex and iterative�…
encoded features. Improving the biological accuracy of annotation is a complex and iterative�…
[CITATION][C] What we do not know about sequence analysis and sequence databases.
PD Karp�- Bioinformatics (Oxford, England), 1998 - academic.oup.com
The marriage of high-throughput nucleotide sequencing with computational methods for the
analysis of nucleotide and protein sequences have ushered in a new era of molecular�…
analysis of nucleotide and protein sequences have ushered in a new era of molecular�…
Pyicos: a versatile toolkit for the analysis of high-throughput sequencing data
S Althammer, J Gonz�lez-Vallinas, C Ballar�…�- …, 2011 - academic.oup.com
Motivation: High-throughput sequencing (HTS) has revolutionized gene regulation studies
and is now fundamental for the detection of protein–DNA and protein–RNA binding, as well�…
and is now fundamental for the detection of protein–DNA and protein–RNA binding, as well�…
Integrated annotation and analysis of genetic variants from next-generation sequencing studies with variant tools
Motivation: Storing, annotating and analyzing variants from next-generation sequencing
projects can be difficult due to the availability of a wide array of data formats, tools and�…
projects can be difficult due to the availability of a wide array of data formats, tools and�…
The Sequence Read Archive: a decade more of explosive growth
K Katz, O Shutov, R Lapoint, M Kimelman…�- Nucleic acids�…, 2022 - academic.oup.com
Abstract The Sequence Read Archive (SRA, https://www. ncbi. nlm. nih. gov/sra/) stores raw
sequencing data and alignment information to enhance reproducibility and facilitate new�…
sequencing data and alignment information to enhance reproducibility and facilitate new�…
[CITATION][C] The challenges of genome sequence annotation or “the devil is in the details”
TF Smith, X Zhang�- Nature Biotechnology, 1997 - nature.com
Two powerful, competing pressures are acting on various genome sequencing projects:
One, to release new sequences as quickly as possible; and two, to provide them with�…
One, to release new sequences as quickly as possible; and two, to provide them with�…
[HTML][HTML] ITSxpress: Software to rapidly trim internally transcribed spacer sequences with quality scores for marker gene analysis
The internally transcribed spacer (ITS) region between the small subunit ribosomal RNA
gene and large subunit ribosomal RNA gene is a widely used phylogenetic marker for fungi�…
gene and large subunit ribosomal RNA gene is a widely used phylogenetic marker for fungi�…