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Investigating the impact of database choice on the accuracy of metagenomic read classification for the rumen microbiome
Microbiome analysis is quickly moving towards high-throughput methods such as metagenomic sequencing. Accurate taxonomic classification of...
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OysterDB: A Genome Database for Ostreidae
The molluscan family Ostreidae, commonly known as oysters, is an important molluscan group due to its economic and ecological importance. In recent...
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HIHISIV: a database of gene expression in HIV and SIV host immune response
In the battle of the host against lentiviral pathogenesis, the immune response is crucial. However, several questions remain unanswered about the...
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G4Bank: A database of experimentally identified DNA G-quadruplex sequences
G-quadruplex (G4), a non-canonical nucleic acid structure, has been suggested to play a key role in important cellular processes including...
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TephritidBase: a genome visualization and gene expression database for tephritid flies
The fruit flies in Tephritidae include many severe fruits and vegetables pests. To date, the genomes and transcriptomes of tephritid flies are...
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Omic horizon expression: a database of gene expression based on RNA sequencing data
BackgroundGene expression profiles have important significance for gene expression characteristics and further functional studies. More attention has...
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Use of a taxon-specific reference database for accurate metagenomics-based pathogen detection of Listeria monocytogenes in turkey deli meat and spinach
BackgroundThe reliability of culture-independent pathogen detection in foods using metagenomics is contingent on the quality and composition of the...
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A large-scale genomically predicted protein mass database enables rapid and broad-spectrum identification of bacterial and archaeal isolates by mass spectrometry
MALDI-TOF MS-based microbial identification relies on reference spectral libraries, which limits the screening of diverse isolates, including...
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SeqWiz: a modularized toolkit for next-generation protein sequence database management and analysis
BackgroundCurrent proteomic technologies are fast-evolving to uncover the complex features of sequence processes, variations and modifications. Thus,...
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Centrifuger: lossless compression of microbial genomes for efficient and accurate metagenomic sequence classification
Centrifuger is an efficient taxonomic classification method that compares sequencing reads against a microbial genome database. In Centrifuger, the...
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Building the Chordata Olfactory Receptor Database using more than 400,000 receptors annotated by Genome2OR
Olfactory receptors are poorly annotated for most genome-sequenced chordates. To address this deficiency, we developed a nhmmer-based olfactory...
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RabbitTClust: enabling fast clustering analysis of millions of bacteria genomes with MinHash sketches
We present RabbitTClust, a fast and memory-efficient genome clustering tool based on sketch-based distance estimation. Our approach enables efficient...
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Ribovore: ribosomal RNA sequence analysis for GenBank submissions and database curation
BackgroundThe DNA sequences encoding ribosomal RNA genes (rRNAs) are commonly used as markers to identify species, including in metagenomics samples...
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Impact of gene annotation choice on the quantification of RNA-seq data
BackgroundRNA sequencing is currently the method of choice for genome-wide profiling of gene expression. A popular approach to quantify expression...
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Canis MitoSNP database: a functional tool useful for comparative analyses of human and canine mitochondrial genomes
Canis MitoSNP is a tool allowing assignment of each mitochondrial genomic position a corresponding position in the mitochondrial gene and in the...
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Structural and Functional Annotation of the Wheat Genome
Wheat genome sequencing has passed through major steps in a decade, starting from the sequencing of large contiguous sequences obtained from...
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CHESS 3: an improved, comprehensive catalog of human genes and transcripts based on large-scale expression data, phylogenetic analysis, and protein structure
CHESS 3 represents an improved human gene catalog based on nearly 10,000 RNA-seq experiments across 54 body sites. It significantly improves current...
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Rapid and sensitive detection of genome contamination at scale with FCS-GX
Assembled genome sequences are being generated at an exponential rate. Here we present FCS-GX, part of NCBI’s Foreign Contamination Screen (FCS) tool...
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Public Domain Databases: A Gold Mine for Identification and Genome Reconstruction of Plant Viruses and Viroids
Plant viruses deprive the host due to their replication in the infected cells by hijacking the host machinery and thereby affecting the quality and...
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A standardized archaeal taxonomy for the Genome Taxonomy Database
The accrual of genomic data from both cultured and uncultured microorganisms provides new opportunities to develop systematic taxonomies based on...
