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Varlociraptor: enhancing sensitivity and controlling false discovery rate in somatic indel discovery
Accurate discovery of somatic variants is of central importance in cancer research. However, count statistics on discovered somatic insertions and...
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Exonuclease editor promotes precision of gene editing in mammalian cells
BackgroundMany efforts have been made to improve the precision of Cas9-mediated gene editing through increasing knock-in efficiency and decreasing...
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Characterisation of Single Nucleotide Polymorphisms and Haplotypes of MSTN Associated with Growth Traits in European Sea Bass (Dicentrarchus labrax)
The myostatin ( MSTN ) gene, known as growth differentiation factor-8 (GDF-8), is a member of the transforming growth factor-β (TGF-β) superfamily and...
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Removing reference bias and improving indel calling in ancient DNA data analysis by map** to a sequence variation graph
BackgroundDuring the last decade, the analysis of ancient DNA (aDNA) sequence has become a powerful tool for the study of past human populations....
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Insertion and deletion mutations preserved in SARS-CoV-2 variants
The insertion/deletion (indel) mutation profiles of SARS-CoV-2 variants, including Omicron, remain unclear. We compared whole-genome sequences from...
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A transcription factor ZmGLK36 confers broad resistance to maize rough dwarf disease in cereal crops
Maize rough dwarf disease (MRDD), caused by maize rough dwarf virus (MRDV) or rice black-streaked dwarf virus (RBSDV), seriously threatens worldwide...
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A hybrid and scalable error correction algorithm for indel and substitution errors of long reads
BackgroundLong-read sequencing has shown the promises to overcome the short length limitations of second-generation sequencing by providing more...
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Development of Indel markers for the selection of Satsuma mandarin (Citrus unshiu Marc.) hybrids that can be used for low-cost genoty** with agarose gels
Cross-breeding between cultivars of Satsuma mandarins is difficult because of the seeds’ polyembryonic characteristics. Even if a seed is obtained by...
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Fine-map** and identification of candidate causal genes for tail length in the Merinolandschaf breed
Docking the tails of lambs in long-tailed sheep breeds is a common practice worldwide. But this practice is associated with pain. Breeding for a...
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QTL map** and candidate gene analysis for yield and grain weight/size in Tartary buckwheat
BackgroundGrain weight/size influences not only grain yield (GY) but also nutritional and appearance quality and consumer preference in Tartary...
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Detection of 40 bp tandem repeat motif and associated insertions and deletions (INDEL) in the mitochondrial DNA control region of Sambar deer (Rusa unicolor)
Sambar ( Rusa unicolor ) is the largest oriental deer and has a wide distribution across South and Southeast Asia. Despite its wide distribution range,...
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Discovery of DNA polymorphisms via genome-resequencing and development of molecular markers between two barley cultivars
Key messageGenome resequencing uncovers genome-wide DNA polymorphisms that are useful for the development of high-density InDel markers between two...
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Scalable Nanopore sequencing of human genomes provides a comprehensive view of haplotype-resolved variation and methylation
Long-read sequencing technologies substantially overcome the limitations of short-reads but have not been considered as a feasible replacement for...
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Assessing sequence variation, haplotype analysis and molecular characterisation of aspartate kinase2 (ask2) gene regulating methionine biosynthesis in diverse maize inbreds
Traditional maize grain is deficient in methionine, an essential amino acid required for proper growth and development in humans and poultry birds....
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Indel marker analysis of putative stress-related genes reveals genetic diversity and differentiation of rice landraces in peninsular Thailand
Genetic assessment of rice landraces is important for germplasm evaluation and genetic resource utilization. Rice landraces in peninsular Thailand...
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nPoRe: n-polymer realigner for improved pileup-based variant calling
Despite recent improvements in nanopore basecalling accuracy, germline variant calling of small insertions and deletions (INDELs) remains poor....
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Identification of a major and stable QTL on chromosome 5A confers spike length in wheat (Triticum aestivum L.)
Spike length (SL) is the key determinant of plant architecture and yield potential. In this study, 193 recombinant inbred lines (RILs) derived from a...
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Sex-Associated SNP Confirmation of Sex-Reversed Male Farmed Japanese Flounder Paralichthys olivaceus
Female Japanese flounder Paralichthys olivaceus grow more rapidly than the male. The goal of all-female commercial production requires an efficient...
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Precision map** and expression analysis of recessive bacterial blight resistance gene xa-45(t) from Oryza glaberrima
BackgroundBacterial blight, caused by Xanthomonas oryzae pv. oryzae ( Xoo ), is one of the most devastating diseases of rice leading to huge yield...
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Hybrid-hybrid correction of errors in long reads with HERO
Although generally superior, hybrid approaches for correcting errors in third-generation sequencing (TGS) reads, using next-generation sequencing...
