In: 2017 IEEE international conference on bioinformatics and biomedicine (BIBM), pp 2226–2228. īehera S, Voshall A, Deogun JS, Moriyama EN (2017) Performance comparison and an ensemble approach of transcriptome assembly. īayer PE, Edwards D, Batley J (2018) Bias in resistance gene prediction due to repeat masking. Nucleic Acids Res 28:45–48īankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS et al (2012) SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. īairoch A, Apweiler R (2000) The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. īaasner J-S, Howard D, Pucker B (2019) Influence of neighboring small sequence variants on functional impact prediction. Accessed on Īnders S, Pyl PT, Huber W (2015) HTSeq-a python framework to work with high-throughput sequencing data. Īndrews S (2010) FastQC a quality control tool for high throughput sequence data. Īlonso-Blanco C, Andrade J, Becker C, Bemm F, Bergelson J, Borgwardt KM et al (2016) 1135 Genomes reveal the global pattern of polymorphism in Arabidopsis thaliana. for the identification of transcripts abundance between different tissues, conditions, or genotypes.Ībe A, Kosugi S, Yoshida K, Natsume S, Takagi H, Kanzaki H et al (2012) Genome sequencing reveals agronomically important loci in rice using MutMap. RNA-Seq reads can be subjected to transcriptome assembly or gene expression analysis, e.g. Transcript abundance is measured via sequencing of the corresponding cDNA molecules. These genomic approaches are complemented by various transcriptomic methods dominated by a very popular RNA-Seq technology. Several mapping-by-sequencing approaches were developed to find underlying genes for relevant traits in crops. Sequence variants can be harnessed for the genetic mapping of traits. Identification of these variants requires sophisticated bioinformatic tools and many of them were developed during past years.
This helps in revealing single nucleotide variants, insertions and deletions, and larger structural variants like inversions and transpositions. Once a high-quality sequence and annotation is available for a species, diversity between accessions can be assessed by re-sequencing. Although these methods were improved substantially over the last years, incorporation of external hints like RNA-Seq reads is beneficial. After generating a genome sequence, gene prediction and the generation of functional annotations are the major challenges. genome-wide investigations of gene families. The availability of a reference genome sequence for a species enables and supports numerous wet lab analyses and comprehensive bioinformatic investigations e.g. Genome assemblies provide details about genes, transposable elements, and the general genome structure. Recent progress in sequencing technologies facilitates plant science experiments through the availability of genome and transcriptome sequences.
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