MITGARD: an automated pipeline for mitochondrial genome assembly in eukaryotic species using RNA-seq data
Sign Up to like & getrecommendations! Published in 2021 at "Briefings in bioinformatics"
DOI: 10.1093/bib/bbaa429
Abstract: MOTIVATION Over the past decade, the field of next-generation sequencing (NGS) has seen dramatic advances in methods and a decrease in costs. Consequently, a large expansion of data has been generated by NGS, most of… read more here.
Keywords: seq; mitgard automated; automated pipeline; mitochondrial genome ... See more keywords
MutateX: an automated pipeline for in silico saturation mutagenesis of protein structures and structural ensembles
Sign Up to like & getrecommendations! Published in 2022 at "Briefings in bioinformatics"
DOI: 10.1093/bib/bbac074
Abstract: Mutations, which result in amino acid substitutions, influence the stability of proteins and their binding to biomolecules. A molecular understanding of the effects of protein mutations is both of biotechnological and medical relevance. Empirical free… read more here.
Keywords: automated pipeline; saturation mutagenesis; silico saturation; protein ... See more keywords
COInr and mkCOInr: Building and customizing a nonredundant barcoding reference database from BOLD and NCBI using a semi‐automated pipeline
Sign Up to like & getrecommendations! Published in 2023 at "Molecular Ecology Resources"
DOI: 10.1111/1755-0998.13756
Abstract: Reference databases with wide taxonomic coverage are greatly needed in many fields of biology, most particularly for the taxonomic assignment of metabarcoding sequences. Therefore, it is fundamental to be able to access and pool data… read more here.
Keywords: database; reference; automated pipeline; semi automated ... See more keywords
StructRNAfinder: an automated pipeline and web server for RNA families prediction
Sign Up to like & getrecommendations! Published in 2018 at "BMC Bioinformatics"
DOI: 10.1186/s12859-018-2052-2
Abstract: BackgroundThe function of many noncoding RNAs (ncRNAs) depend upon their secondary structures. Over the last decades, several methodologies have been developed to predict such structures or to use them to functionally annotate RNAs into RNA… read more here.
Keywords: prediction; automated pipeline; structrnafinder; rna families ... See more keywords
A fully automated pipeline for quantitative genotype calling from next generation sequencing data in autopolyploids
Sign Up to like & getrecommendations! Published in 2018 at "BMC Bioinformatics"
DOI: 10.1186/s12859-018-2433-6
Abstract: BackgroundGenotyping-by-sequencing (GBS) has been used broadly in genetic studies for several species, especially those with agricultural importance. However, its use is still limited in autopolyploid species because genotype calling software generally fails to properly distinguish… read more here.
Keywords: genotype calling; automated pipeline; fully automated; quantitative genotype ... See more keywords
An automated pipeline for bouton, spine, and synapse detection of in vivo two-photon images
Sign Up to like & getrecommendations! Published in 2017 at "BioData Mining"
DOI: 10.1186/s13040-017-0161-5
Abstract: BackgroundIn the nervous system, the neurons communicate through synapses. The size, morphology, and connectivity of these synapses are significant in determining the functional properties of the neural network. Therefore, they have always been a major… read more here.
Keywords: photon; two photon; automated pipeline; photon images ... See more keywords
ASPICov: An automated pipeline for identification of SARS-Cov2 nucleotidic variants
Sign Up to like & getrecommendations! Published in 2022 at "PLoS ONE"
DOI: 10.1371/journal.pone.0262953
Abstract: ASPICov was developed to provide a rapid, reliable and complete analysis of NGS SARS-Cov2 samples to the biologist. This broad application tool allows to process samples from either capture or amplicon strategy and Illumina or… read more here.
Keywords: sars cov2; pipeline; identification sars; pipeline identification ... See more keywords