Demand for larger Y-STR reference databases in ethnic melting-pot countries: Argentina as a test case
Sign Up to like & getrecommendations! Published in 2019 at "International Journal of Legal Medicine"
DOI: 10.1007/s00414-019-02012-5
Abstract: The Y chromosome behaves as a single locus. Its genetic information is useful in forensic casework, deficiency kinship testing, and population genetics studies. Continuous increases of loci number within commercial kits forced modification of worldwide… read more here.
Keywords: demand larger; larger str; databases ethnic; reference databases ... See more keywords
Anacapa Toolkit: An environmental DNA toolkit for processing multilocus metabarcode datasets
Sign Up to like & getrecommendations! Published in 2019 at "Methods in Ecology and Evolution"
DOI: 10.1111/2041-210x.13214
Abstract: Environmental DNA (eDNA) metabarcoding is a promising method to monitor species and community diversity that is rapid, affordable and non‐invasive. The longstanding needs of the eDNA community are modular informatics tools, comprehensive and customizable reference… read more here.
Keywords: metabarcode; anacapa toolkit; toolkit; reference databases ... See more keywords
Generation of Comprehensive Ecosystem-Specific Reference Databases with Species-Level Resolution by High-Throughput Full-Length 16S rRNA Gene Sequencing and Automated Taxonomy Assignment (AutoTax)
Sign Up to like & getrecommendations! Published in 2020 at "mBio"
DOI: 10.1128/mbio.01557-20
Abstract: High-throughput 16S rRNA gene amplicon sequencing is an essential method for studying the diversity and dynamics of microbial communities. However, this method is presently hampered by the lack of high-identity reference sequences for many environmental… read more here.
Keywords: 16s rrna; reference; reference databases; rrna gene ... See more keywords
The use of taxon-specific reference databases compromises metagenomic classification
Sign Up to like & getrecommendations! Published in 2020 at "BMC Genomics"
DOI: 10.1186/s12864-020-6592-2
Abstract: A recent article in BMC Genomics describes a new bioinformatics tool, HumanMycobiomeScan, to classify fungal taxa in metagenomic samples. This tool was used to characterize the gut mycobiome of hunter-gatherers and Western populations, resulting in… read more here.
Keywords: taxon specific; classification; reference databases; reference ... See more keywords
Application of ecosystem-specific reference databases for increased taxonomic resolution in soil microbial profiling
Sign Up to like & getrecommendations! Published in 2022 at "Frontiers in Microbiology"
DOI: 10.3389/fmicb.2022.942396
Abstract: Intensive agriculture systems have paved the way for a growing human population. However, the abundant use of mineral fertilizers and pesticides may negatively impact nutrient cycles and biodiversity. One potential alternative is to harness beneficial… read more here.
Keywords: reference; ecosystem specific; reference databases; taxonomic resolution ... See more keywords
Be positive: customized reference databases and new, local barcodes balance false taxonomic assignments in metabarcoding studies
Sign Up to like & getrecommendations! Published in 2023 at "PeerJ"
DOI: 10.7717/peerj.14616
Abstract: Background In metabarcoding analyses, the taxonomic assignment is crucial to place sequencing data in biological and ecological contexts. This fundamental step depends on a reference database, which should have a good taxonomic coverage to avoid… read more here.
Keywords: reference database; reference databases; taxonomic assignment; database ... See more keywords