Analysis of Plant Pan-Genomes and Transcriptomes with GET_HOMOLOGUES-EST, a Clustering Solution for Sequences of the Same Species
出版年份 2017 全文链接
标题
Analysis of Plant Pan-Genomes and Transcriptomes with GET_HOMOLOGUES-EST, a Clustering Solution for Sequences of the Same Species
作者
关键词
-
出版物
Frontiers in Plant Science
Volume 8, Issue -, Pages -
出版商
Frontiers Media SA
发表日期
2017-02-14
DOI
10.3389/fpls.2017.00184
参考文献
相关参考文献
注意:仅列出部分参考文献,下载原文获取全部文献信息。- PanTools: representation, storage and exploration of pan-genomic data
- (2016) Siavash Sheikhizadeh et al. BIOINFORMATICS
- RapMap: a rapid, sensitive and accurate tool for mapping RNA-seq reads to transcriptomes
- (2016) Avi Srivastava et al. BIOINFORMATICS
- Computational pan-genomics: status, promises and challenges
- (2016) BRIEFINGS IN BIOINFORMATICS
- 1,135 Genomes Reveal the Global Pattern of Polymorphism in Arabidopsis thaliana
- (2016) Carlos Alonso-Blanco et al. CELL
- Genome-wide association study using whole-genome sequencing rapidly identifies new genes influencing agronomic traits in rice
- (2016) Kenji Yano et al. NATURE GENETICS
- Integrative approaches for large-scale transcriptome-wide association studies
- (2016) Alexander Gusev et al. NATURE GENETICS
- The pangenome of an agronomically important crop plant Brassica oleracea
- (2016) Agnieszka A. Golicz et al. Nature Communications
- Maize pan-transcriptome provides novel insights into genome complexity and quantitative trait variation
- (2016) Minliang Jin et al. Scientific Reports
- A Cluster of Nucleotide-Binding Site–Leucine-Rich Repeat Genes Resides in a Barley Powdery Mildew Resistance Quantitative Trait Loci on 7HL
- (2016) Carlos P. Cantalapiedra et al. Plant Genome
- The Arabidopsis thaliana mobilome and its impact at the species level
- (2016) Leandro Quadrana et al. eLife
- Cnidaria: fast, reference-free clustering of raw and assembled genome and transcriptome NGS data
- (2015) Saulo Alves Aflitos et al. BMC BIOINFORMATICS
- Improvement of barley genome annotations by deciphering the Haruna Nijo genome
- (2015) Kazuhiro Sato et al. DNA RESEARCH
- The Pfam protein families database: towards a more sustainable future
- (2015) Robert D. Finn et al. NUCLEIC ACIDS RESEARCH
- Towards plant pangenomics
- (2015) Agnieszka A. Golicz et al. PLANT BIOTECHNOLOGY JOURNAL
- High-resolution genetic mapping of maize pan-genome sequence anchors
- (2015) Fei Lu et al. Nature Communications
- A Brief Review of Software Tools for Pangenomics
- (2015) Jingfa Xiao et al. GENOMICS PROTEOMICS & BIOINFORMATICS
- Trimmomatic: a flexible trimmer for Illumina sequence data
- (2014) Anthony M. Bolger et al. BIOINFORMATICS
- Structural variation and genome complexity: is dispensable really dispensable?
- (2014) Fabio Marroni et al. CURRENT OPINION IN PLANT BIOLOGY
- Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes
- (2014) M. Kim et al. INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
- Dynamic evolution of NBS–LRR genes in bread wheat and its progenitors
- (2014) Longjiang Gu et al. MOLECULAR GENETICS AND GENOMICS
- De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits
- (2014) Ying-hui Li et al. NATURE BIOTECHNOLOGY
- Fast and sensitive protein alignment using DIAMOND
- (2014) Benjamin Buchfink et al. NATURE METHODS
- Insights into the Maize Pan-Genome and Pan-Transcriptome
- (2014) C. N. Hirsch et al. PLANT CELL
- Transcriptome profiling reveals mosaic genomic origins of modern cultivated barley
- (2014) Fei Dai et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- GET_HOMOLOGUES, a Versatile Software Package for Scalable and Robust Microbial Pangenome Analysis
- (2013) Bruno Contreras-Moreira et al. APPLIED AND ENVIRONMENTAL MICROBIOLOGY
- Presence–Absence Variation in A. thaliana Is Primarily Associated with Genomic Signatures Consistent with Relaxed Selective Constraints
- (2013) Stephen J. Bush et al. MOLECULAR BIOLOGY AND EVOLUTION
- De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis
- (2013) Brian J Haas et al. Nature Protocols
- Resistance gene enrichment sequencing (RenSeq) enables reannotation of the NB-LRR gene family from sequenced plant genomes and rapid mapping of resistance loci in segregating populations
- (2013) Florian Jupe et al. PLANT JOURNAL
- Musket: a multistage k-mer spectrum-based error corrector for Illumina sequence data
- (2012) Yongchao Liu et al. BIOINFORMATICS
- How important are transposons for plant evolution?
- (2012) Damon Lisch NATURE REVIEWS GENETICS
- Structural Variants in the Soybean Genome Localize to Clusters of Biotic Stress-Response Genes
- (2012) L. K. McHale et al. PLANT PHYSIOLOGY
- Maize (Zea mays L.) Genome Diversity as Revealed by RNA-Sequencing
- (2012) Candice N. Hansey et al. PLoS One
- Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega
- (2011) F. Sievers et al. Molecular Systems Biology
- Multiple reference genomes and transcriptomes for Arabidopsis thaliana
- (2011) Xiangchao Gan et al. NATURE
- Whole-genome sequencing of multiple Arabidopsis thaliana populations
- (2011) Jun Cao et al. NATURE GENETICS
- Pan-genome sequence analysis using Panseq: an online tool for the rapid analysis of core and accessory genomic regions
- (2010) Chad Laing et al. BMC BIOINFORMATICS
- Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
- (2010) Cole Trapnell et al. NATURE BIOTECHNOLOGY
- Genome-wide patterns of genetic variation among elite maize inbred lines
- (2010) Jinsheng Lai et al. NATURE GENETICS
- TopHat: discovering splice junctions with RNA-Seq
- (2009) Cole Trapnell et al. BIOINFORMATICS
- BLAST+: architecture and applications
- (2009) Christiam Camacho et al. BMC BIOINFORMATICS
- Building the sequence map of the human pan-genome
- (2009) Ruiqiang Li et al. NATURE BIOTECHNOLOGY
- primers4clades: a web server that uses phylogenetic trees to design lineage-specific PCR primers for metagenomic and diversity studies
- (2009) B. Contreras-Moreira et al. NUCLEIC ACIDS RESEARCH
- Maize Inbreds Exhibit High Levels of Copy Number Variation (CNV) and Presence/Absence Variation (PAV) in Genome Content
- (2009) Nathan M. Springer et al. PLoS Genetics
- Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world
- (2008) E. V. Koonin et al. NUCLEIC ACIDS RESEARCH
Publish scientific posters with Peeref
Peeref publishes scientific posters from all research disciplines. Our Diamond Open Access policy means free access to content and no publication fees for authors.
Learn MoreBecome a Peeref-certified reviewer
The Peeref Institute provides free reviewer training that teaches the core competencies of the academic peer review process.
Get Started