Complete reannotation of the Arabidopsis genome: methods, tools, protocols and the final release (Q24804698)

2 July 2017

title

Complete reannotation of the Arabidopsis genome: methods, tools, protocols and the final release (English)

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2 July 2017

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2 July 2017

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2 July 2017

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Chunhui Yu

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2 July 2017

Brian J Haas

1

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2 July 2017

Catherine M Ronning

3

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2 July 2017

Roger K Smith

5

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2 July 2017

Rama Maiti

6

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2 July 2017

Agnes P Chan

7

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2 July 2017

Maryam Farzad

9

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2 July 2017

Dongying Wu

10

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2 July 2017

Owen White

11

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2 July 2017

Christopher D Town

12

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2 July 2017

language of work or name

English

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publication date

22 March 2005

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2 July 2017

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2 July 2017

volume

3

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2 July 2017

issue

1

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page(s)

7

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Creative Commons Attribution 2.0 Generic

2 July 2017

copyright license

start time

22 March 2005

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April 2022 Public Data File from Crossref

copyright status

copyrighted

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April 2022 Public Data File from Crossref

describes a project that uses

MUMmer

object named as

MUMMER

1 reference

CZ Software Mentions: A large dataset of software mentions in the biomedical literature

cites work

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7 April 2017

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7 April 2017

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7 April 2017

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7 April 2017

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Full-length messenger RNA sequences greatly improve genome annotation

7 April 2017

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7 April 2017

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7 April 2017

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7 April 2017

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7 April 2017

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7 April 2017

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7 April 2017

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CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice

7 April 2017

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Analysis of the genome sequence of the flowering plant Arabidopsis thaliana

7 April 2017

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The Gene Ontology (GO) database and informatics resource

7 April 2017

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Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes

7 April 2017

1 reference

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Profile hidden Markov models

7 April 2017

1 reference

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Prediction of complete gene structures in human genomic DNA

7 April 2017

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Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1082884

Empirical analysis of transcriptional activity in the Arabidopsis genome

7 April 2017

1 reference

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Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events

7 April 2017

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The InterPro database, 2003 brings increased coverage and new features

7 April 2017

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Experimental RNomics: identification of 140 candidates for small non-messenger RNAs in the plant Arabidopsis thaliana

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1082884

Antisense transcripts in the human genome

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1082884

The leucine-rich repeat as a protein recognition motif

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1082884

Predicting subcellular localization of proteins based on their N-terminal amino acid sequence

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1082884

Do natural antisense transcripts make sense in eukaryotes?

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1082884

Functional annotation of the Arabidopsis genome using controlled vocabularies

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1082884

InterProScan--an integration platform for the signature-recognition methods in InterPro

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1082884

Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1082884

A computer program for aligning a cDNA sequence with a genomic DNA sequence

7 April 2017

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Does this have a familiar RING?

7 April 2017

1 reference

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The use of MPSS for whole-genome transcriptional analysis in Arabidopsis

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1082884

Annotation of parasite genomes

28 September 2017

1 reference

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Supra-domains: evolutionary units larger than single protein domains

28 September 2017

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The Gene Ontology Annotation (GOA) Database--an integrated resource of GO annotations to the UniProt Knowledgebase

28 September 2017

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Whole genome sequence comparisons and "full-length" cDNA sequences: a combined approach to evaluate and improve Arabidopsis genome annotation

28 September 2017

1 reference

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EyeSite: a semi-automated database of protein families in the eye.

28 September 2017

1 reference

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Recent improvements to the PROSITE database

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1082884

Database and analyses of known alternatively spliced genes in plants

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1082884

Alternative splicing and proteome diversity in plants: the tip of the iceberg has just emerged

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1082884

Protein families and TRIBES in genome sequence space

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1082884

Comparative genomics of Physcomitrella patens gametophytic transcriptome and Arabidopsis thaliana: implication for land plant evolution

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1082884

Apparent homology of expressed genes from wood-forming tissues of loblolly pine (Pinus taeda L.) with Arabidopsis thaliana

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1082884

Comparisons with Caenorhabditis (approximately 100 Mb) and Drosophila (approximately 175 Mb) using flow cytometry show genome size in Arabidopsis to be approximately 157 Mb and thus approximately 25% larger than the Arabidopsis genome initiative est

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1082884

A recent polyploidy superimposed on older large-scale duplications in the Arabidopsis genome

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1082884

PRINTS and its automatic supplement, prePRINTS.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1082884

A global analysis of Caenorhabditis elegans operons

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1082884

Alternative splicing: combinatorial output from the genome

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1082884

Functional annotation of a full-length Arabidopsis cDNA collection

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1082884

Computational gene finding in plants

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1082884

Alternative splicing and genome complexity

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1082884

Gene and genome duplication

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1082884

GeneSplicer: a new computational method for splice site prediction

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1082884

The sense of naturally transcribed antisense RNAs in plants

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1082884

Machine learning approaches for the prediction of signal peptides and other protein sorting signals

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1082884

A Tool for Analyzing and Annotating Genomic Sequences

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1082884

The stoned locus of Drosophila melanogaster produces a dicistronic transcript and encodes two distinct polypeptides.

28 September 2017

1 reference

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RPS4-mediated disease resistance requires the combined presence of RPS4 transcripts with full-length and truncated open reading frames

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1082884

Identification and analysis of Arabidopsis expressed sequence tags characteristic of non-coding RNAs

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1082884

Polycistronic expression and RNA-binding specificity of the C. elegans homologue of the spliceosome-associated protein SAP49.

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1082884

A new algorithm for best subsequence alignments with application to tRNA-rRNA comparisons

30 May 2018

1 reference

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DAGchainer: a tool for mining segmental genome duplications and synteny

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1082884

Development and evaluation of an Arabidopsis whole genome Affymetrix probe array

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1082884

The subcellular localization of plant protein phosphatase 5 isoforms is determined by alternative splicing

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1082884

Refined annotation of the Arabidopsis genome by complete expressed sequence tag mapping

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1082884

Annotation of the Arabidopsis genome

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1082884

ProDom: automated clustering of homologous domains

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1082884

Functional significance of the alternative transcript processing of the Arabidopsis floral promoter FCA.

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1082884

Multiple forms of formamidopyrimidine-DNA glycosylase produced by alternative splicing in Arabidopsis thaliana

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1082884

The Arabidopsis splicing factor SR1 is regulated by alternative splicing.

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1082884

Alternative splicing of pre-mRNA: developmental consequences and mechanisms of regulation

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1082884

Gene clusters and polycistronic transcription in eukaryotes.

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1082884

Cyclophilin and Protein Disulfide Isomerase Genes Are Co-Transcribed in a Functionally Related Manner inCaenorhabditis elegans

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1082884

On global sequence alignment.

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1082884

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1082884

Detection of Arabidopsis thaliana AtRAD1 cDNA variants and assessment of function by expression in a yeast rad1 mutant

28 November 2018

1 reference

12 December 2020

Exploitation of colinear relationships between the genomes of Lotus japonicus, Pisum sativum and Arabidopsis thaliana, for positional cloning of a legume symbiosis gene

1 reference

12 December 2020

Arabidopsis thaliana Centromere Regions: Genetic Map Positions and Repetitive DNA Structure

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12 December 2020

An intragenic suppressor of the Arabidopsis floral organ identity mutant apetala3-1 functions by suppressing defects in splicing

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12 December 2020

Light regulates alternative splicing of hydroxypyruvate reductase in pumpkin

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12 December 2020

Reducing the space requirement of suffix trees

1 reference

Crossref

https://api.crossref.org/works/10.1186/1741-7007-3-7

7 January 2021

https://api.crossref.org/works/10.1186/1741-7007-3-7

1 reference

7 January 2021

Does this have a familiar RING?

1 reference

Crossref

https://api.crossref.org/works/10.1186/1741-7007-3-7

7 January 2021

THE DISTRIBUTION OF THE FLORA IN THE ALPINE ZONE.1

1 reference

Crossref

https://api.crossref.org/works/10.1186/1741-7007-3-7

7 January 2021

Identifiers

DOI

10.1186/1741-7007-3-7

1 reference

Dimensions Publication ID

2 July 2017

1011930742

0 references

PMC publication ID

1082884

0 references

1 reference