(Q42778174)

6 March 2018

title

Genome re-annotation of the wild strawberry Fragaria vesca using extensive Illumina- and SMRT-based RNA-seq datasets (English)

1 reference

6 March 2018

0 references

1 reference

1 reference

Yongping Li

1

1 reference

6 March 2018

Wei Wei

2

1 reference

6 March 2018

Jia Feng

3

1 reference

6 March 2018

Huifeng Luo

4

1 reference

6 March 2018

Mengting Pi

5

1 reference

6 March 2018

Zhongchi Liu

6

1 reference

6 March 2018

Chunying Kang

7

1 reference

6 March 2018

publication date

23 September 2017

1 reference

6 March 2018

published in

DNA Research

1 reference

6 March 2018

FEELnc: a tool for long non-coding RNA annotation and its application to the dog transcriptome

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27 May 2018

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27 May 2018

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Reprogramming of Strawberry (Fragaria vesca) Root Transcriptome in Response to Phytophthora cactorum

27 May 2018

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Genome-scale DNA variant analysis and functional validation of a SNP underlying yellow fruit color in wild strawberry

27 May 2018

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Single-molecule real-time transcript sequencing facilitates common wheat genome annotation and grain transcriptome research

27 May 2018

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Global identification and analysis of long non-coding RNAs in diploid strawberry Fragaria vesca during flower and fruit development

27 May 2018

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Exploiting single-molecule transcript sequencing for eukaryotic gene prediction

27 May 2018

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Comprehensive Annotation of Physcomitrella patens Small RNA Loci Reveals That the Heterochromatic Short Interfering RNA Pathway Is Largely Conserved in Land Plants.

27 May 2018

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Novel and Recently Evolved MicroRNA Clusters Regulate Expansive F-BOX Gene Networks through Phased Small Interfering RNAs in Wild Diploid Strawberry

27 May 2018

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BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

27 May 2018

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Mechanisms and Regulation of Alternative Pre-mRNA Splicing

27 May 2018

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StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

27 May 2018

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Re-annotation of the woodland strawberry (Fragaria vesca) genome

27 May 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5824900

Evolutionary origins and dynamics of octoploid strawberry subgenomes revealed by dense targeted capture linkage maps

27 May 2018

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Fragaria: a genus with deep historical roots and ripe for evolutionary and ecological insights

27 May 2018

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Genome and transcriptome of the porcine whipworm Trichuris suis

27 May 2018

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Floral Transcriptomes in Woodland Strawberry Uncover Developing Receptacle and Anther Gene Networks.

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5824900

InterProScan 5: genome-scale protein function classification

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5824900

Assessment of transcript reconstruction methods for RNA-seq

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5824900

Complexity of the alternative splicing landscape in plants.

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5824900

Web Apollo: a web-based genomic annotation editing platform

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5824900

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5824900

ShortStack: comprehensive annotation and quantification of small RNA genes

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5824900

Mutation in TERMINAL FLOWER1 reverses the photoperiodic requirement for flowering in the wild strawberry Fragaria vesca

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5824900

MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5824900

Full-length transcriptome assembly from RNA-Seq data without a reference genome

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5824900

Integrative genomics viewer

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5824900

The genome of woodland strawberry (Fragaria vesca)

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5824900

Aligning short sequencing reads with Bowtie

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5824900

The Sequence Alignment/Map format and SAMtools

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5824900

Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5824900

CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine.

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5824900

ASTALAVISTA: dynamic and flexible analysis of alternative splicing events in custom gene datasets

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5824900

Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5824900

Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5824900

GMAP: a genomic mapping and alignment program for mRNA and EST sequences

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5824900

Automated generation of heuristics for biological sequence comparison

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5824900

Gene prediction with a hidden Markov model and a new intron submodel

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5824900

Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5824900

The generic genome browser: a building block for a model organism system database

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5824900

Basic local alignment search tool

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5824900

uORF-mediated translation allows engineered plant disease resistance without fitness costs

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5824900

iTAK: A Program for Genome-wide Prediction and Classification of Plant Transcription Factors, Transcriptional Regulators, and Protein Kinases.

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5824900

LoRDEC: accurate and efficient long read error correction.

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5824900

The Fragaria vesca homolog of suppressor of overexpression of constans1 represses flowering and promotes vegetative growth

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5824900

Genome-scale transcriptomic insights into early-stage fruit development in woodland strawberry Fragaria vesca

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5824900

The TFL1 homologue KSN is a regulator of continuous flowering in rose and strawberry.

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5824900

Using native and syntenically mapped cDNA alignments to improve de novo gene finding.

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5824900

Cutadapt removes adapter sequences from high-throughput sequencing reads

16 August 2018

1 reference

Crossref

https://api.crossref.org/works/10.1093%2FDNARES%2FDSX038

21 January 2018

Identifiers

DOI

10.1093/DNARES/DSX038

1 reference

6 March 2018

PMC publication ID

5824900

1 reference

6 March 2018

PubMed publication ID

29036429

1 reference

6 March 2018