LAUSR

Target sequence data shed new light on the infrafamilial classification of Araceae.

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1 Published in 2022 at "American journal of botany"

DOI: 10.1002/ajb2.16117

Abstract: PREMISE Recent phylogenetic studies of the Araceae have confirmed the position of the duckweeds nested within the aroids, and the monophyly of a clade containing all the unisexual flowered aroids plus the bisexual-flowered Calla palustris.… read more here.

Keywords: araceae; sequence; calla; target sequence ... See more keywords

Generating DNA sequence data with limited resources for molecular biology: Lessons from a barcoding project in Indonesia

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0 Published in 2018 at "Applications in Plant Sciences"

DOI: 10.1002/aps3.1167

Abstract: The advent of the DNA sequencing age has led to a revolution in biology. The rapid and cost‐effective generation of high‐quality sequence data has transformed many fields, including those focused on discovering species and surveying… read more here.

Keywords: dna sequence; sequence data; biology; barcoding project ... See more keywords

A genome-wide study of Hardy–Weinberg equilibrium with next generation sequence data

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0 Published in 2017 at "Human Genetics"

DOI: 10.1007/s00439-017-1786-7

Abstract: Statistical tests for Hardy–Weinberg equilibrium have been an important tool for detecting genotyping errors in the past, and remain important in the quality control of next generation sequence data. In this paper, we analyze complete… read more here.

Keywords: hardy weinberg; sequence data; generation sequence; next generation ... See more keywords

Multiple instance learning for sequence data with across bag dependencies

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1 Published in 2020 at "International Journal of Machine Learning and Cybernetics"

DOI: 10.1007/s13042-019-01021-5

Abstract: In Multiple Instance Learning (MIL) problem for sequence data, the instances inside the bags are sequences. In some real world applications such as bioinformatics, comparing a random couple of sequences makes no sense. In fact,… read more here.

Keywords: instance learning; multiple instance; sequence data; across bag ... See more keywords

Prediction of functional metagenomic composition using archived 16S rDNA sequence data from the gut microbiota of livestock

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0 Published in 2018 at "Livestock Science"

DOI: 10.1016/j.livsci.2018.04.017

Abstract: Abstract The volume of microbial genetic terabases in public repositories is getting infamous, yet much of this data has been used only once. On top of this global concern, there is still much to be… read more here.

Keywords: rdna sequence; 16s rdna; livestock; sequence data ... See more keywords

Transcriptome and target DNA enrichment sequence data provide new insights into the phylogeny of vespid wasps (Hymenoptera: Aculeata: Vespidae).

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0 Published in 2017 at "Molecular phylogenetics and evolution"

DOI: 10.1016/j.ympev.2017.08.020

Abstract: The wasp family Vespidae comprises more than 5000 described species which represent life history strategies ranging from solitary and presocial to eusocial and socially parasitic. The phylogenetic relationships of the major vespid wasp lineages (i.e.,… read more here.

Keywords: vespidae; target dna; vespid wasps; sequence data ... See more keywords

Determinants and Prediction of Esterase Substrate Promiscuity Patterns.

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0 Published in 2018 at "ACS chemical biology"

DOI: 10.1021/acschembio.7b00996

Abstract: Esterases receive special attention because of their wide distribution in biological systems and environments and their importance for physiology and chemical synthesis. The prediction of esterases' substrate promiscuity level from sequence data and the molecular… read more here.

Keywords: substrate promiscuity; sequence data; promiscuity; prediction ... See more keywords

General strategies for using amino acid sequence data to guide biochemical investigation of protein function.

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1 Published in 2022 at "Biochemical Society transactions"

DOI: 10.1042/bst20220849

Abstract: The rapid increase of '-omics' data warrants the reconsideration of experimental strategies to investigate general protein function. Studying individual members of a protein family is likely insufficient to provide a complete mechanistic understanding of family… read more here.

Keywords: family; acid sequence; sequence; amino acid ... See more keywords

A pipeline for local assembly of minisatellite alleles from single-molecule sequencing data

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0 Published in 2017 at "Bioinformatics"

DOI: 10.1093/bioinformatics/btw687

Abstract: Motivation: The advent of Next Generation Sequencing (NGS) has led to the generation of enormous volumes of short read sequence data, cheaply and in reasonable time scales. Nevertheless, the quality of genome assemblies generated using… read more here.

Keywords: molecule; molecule sequencing; single molecule; pipeline ... See more keywords

ntEdit: scalable genome sequence polishing

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0 Published in 2019 at "Bioinformatics"

DOI: 10.1093/bioinformatics/btz400

Abstract: Abstract Motivation In the modern genomics era, genome sequence assemblies are routine practice. However, depending on the methodology, resulting drafts may contain considerable base errors. Although utilities exist for genome base polishing, they work best… read more here.

Keywords: genome sequence; sequence data; coverage; ntedit scalable ... See more keywords

Protein contact prediction using metagenome sequence data and residual neural networks

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0 Published in 2020 at "Bioinformatics"

DOI: 10.1093/bioinformatics/btz477

Abstract: MOTIVATION Almost all protein residue contact prediction methods rely on the availability of deep multiple sequence alignments (MSAs). However, many proteins from the poorly populated families do not have sufficient number of homologs in the… read more here.

Keywords: metagenome sequence; neural networks; sequence data; contact prediction ... See more keywords