Efficient assembly and annotation of the transcriptome of catfish by RNA-Seq analysis of a doubled haploid homozygote (Q34467479)

2 August 2017

title

Efficient assembly and annotation of the transcriptome of catfish by RNA-Seq analysis of a doubled haploid homozygote (English)

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2 August 2017

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1

Shikai Liu

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2 August 2017

14

Eric Peatman

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Geoff Waldbieser

4

object named as

Geoff Waldbieser

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Huseyin Kucuktas

13

object named as

Huseyin Kucuktas

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2 August 2017

Yu Zhang

2

1 reference

2 August 2017

Zunchun Zhou

3

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2 August 2017

Geoff Waldbieser

4

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2 August 2017

Fanyue Sun

5

1 reference

2 August 2017

Jianguo Lu

6

1 reference

2 August 2017

Jiaren Zhang

7

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2 August 2017

Yanliang Jiang

8

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2 August 2017

Hao Zhang

9

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2 August 2017

Xiuli Wang

10

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2 August 2017

K V Rajendran

11

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2 August 2017

Lester Khoo

12

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2 August 2017

Zhanjiang Liu

15

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2 August 2017

language of work or name

English

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publication date

5 November 2012

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2 August 2017

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2 August 2017

volume

13

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2 August 2017

page(s)

595

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describes a project that uses

2 August 2017

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The head-regeneration transcriptome of the planarian Schmidtea mediterranea.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3582483

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3582483

De novo assembly and validation of planaria transcriptome by massive parallel sequencing and shotgun proteomics

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3582483

Generation of genome-scale gene-associated SNPs in catfish for the construction of a high-density SNP array

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3582483

De novo assembled expressed gene catalog of a fast-growing Eucalyptus tree produced by Illumina mRNA-Seq.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3582483

De novo assembly and analysis of RNA-seq data.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3582483

Comprehensive annotation of the transcriptome of the human fungal pathogen Candida albicans using RNA-seq

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3582483

Optimization of de novo transcriptome assembly from next-generation sequencing data

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3582483

Identification and characterization of full-length cDNAs in channel catfish (Ictalurus punctatus) and blue catfish (Ictalurus furcatus)

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3582483

Assembly of 500,000 inter-specific catfish expressed sequence tags and large scale gene-associated marker development for whole genome association studies

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3582483

UTRdb and UTRsite (RELEASE 2010): a collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3582483

Characterization of full-length sequenced cDNA inserts (FLIcs) from Atlantic salmon (Salmo salar)

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3582483

Sense from sequence reads: methods for alignment and assembly

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3582483

Production of viable homozygous, doubled haploid channel catfish (Ictalurus punctatus).

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3582483

Benchmarking next-generation transcriptome sequencing for functional and evolutionary genomics

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3582483

Gene discovery using massively parallel pyrosequencing to develop ESTs for the flesh fly Sarcophaga crassipalpis.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3582483

Sequencing and de novo analysis of a coral larval transcriptome using 454 GSFlx

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3582483

Next-generation pyrosequencing of gonad transcriptomes in the polyploid lake sturgeon (Acipenser fulvescens): the relative merits of normalization and rarefaction in gene discovery

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3582483

ABySS: a parallel assembler for short read sequence data

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3582483

Annotating genomes with massive-scale RNA sequencing

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3582483

RNA-Seq: a revolutionary tool for transcriptomics

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3582483

Velvet: algorithms for de novo short read assembly using de Bruijn graphs

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3582483

Rapid transcriptome characterization for a nonmodel organism using 454 pyrosequencing.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3582483

Next-generation sequencing transforms today's biology

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3582483

Gene expression profiling by massively parallel sequencing.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3582483

Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3582483

Characterization of 954 bovine full-CDS cDNA sequences.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3582483

OrfPredictor: predicting protein-coding regions in EST-derived sequences

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3582483

WebLogo: A Sequence Logo Generator

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3582483

CDS annotation in full-length cDNA sequence

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3582483

Reexamining the polyadenylation signal: were we wrong about AAUAAA?

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3582483

Effect of selenium and vitamin E deficiency on differential gene expression in rat liver

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3582483

UAG readthrough in mammalian cells: effect of upstream and downstream stop codon contexts reveal different signals

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3582483

Translational termination comes of age.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3582483

Patterns of variant polyadenylation signal usage in human genes

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3582483

Translation termination in eukaryotes: polypeptide release factor eRF1 is composed of functionally and structurally distinct domains

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3582483

Iron-regulatory proteins, iron-responsive elements and ferritin mRNA translation

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3582483

In silico detection of control signals: mRNA 3'-end-processing sequences in diverse species

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3582483

Identification of RNA-binding surfaces in iron regulatory protein-1.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3582483

Combinatorial pattern discovery in biological sequences: The TEIRESIAS algorithm

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3582483

Selenium and the thioredoxin and glutaredoxin systems

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3582483

Translational termination efficiency in both bacteria and mammals is regulated by the base following the stop codon

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3582483

A novel RNA structural motif in the selenocysteine insertion element of eukaryotic selenoprotein mRNAs

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3582483

Translational termination efficiency in mammals is influenced by the base following the stop codon.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3582483

The efficiency of translation termination is determined by a synergistic interplay between upstream and downstream sequences in Saccharomyces cerevisiae.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3582483

An analysis of 5'-noncoding sequences from 699 vertebrate messenger RNAs

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3582483

Eukaryotic start and stop translation sites.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3582483

6 July 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2164-13-595

Genotype calling and mapping of multisite variants using an Atlantic salmon iSelect SNP array.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2164-13-595

Comparative analysis of base biases around the stop codons in six eukaryotes.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2164-13-595

Expressing the human genome

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2164-13-595

The influence of 5' codon context on translation termination in Saccharomyces cerevisiae

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23127152

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

The selenocysteine insertion sequence binding protein SBP is different from the Y-box protein dbpB

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23127152

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1186/1471-2164-13-595

1 reference

2 August 2017

1 reference

2 August 2017

1 reference