(Q44439585)

3 December 2017

title

MAKER-P: a tool kit for the rapid creation, management, and quality control of plant genome annotations (English)

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3 December 2017

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3 December 2017

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3 December 2017

Gaurav D Moghe

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Kevin L Childs

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Carolyn Lawrence-Dill

Carolyn J Lawrence

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Yanni Sun

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Michael S Campbell

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3 December 2017

MeiYee Law

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3 December 2017

Carson Holt

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3 December 2017

Joshua C Stein

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3 December 2017

David E Hufnagel

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3 December 2017

Rujira Achawanantakun

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3 December 2017

Dian Jiao

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3 December 2017

Doreen Ware

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3 December 2017

Ning Jiang

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3 December 2017

Mark Yandell

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3 December 2017

language of work or name

English

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publication date

4 December 2013

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3 December 2017

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3 December 2017

volume

164

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3 December 2017

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3 December 2017

page(s)

513-524

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Creative Commons Attribution 4.0 International

3 December 2017

start time

25 January 2021

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April 2022 Public Data File from Crossref

copyrighted

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cites work

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Plant-symbiotic fungi as chemical engineers: multi-genome analysis of the clavicipitaceae reveals dynamics of alkaloid loci

27 August 2018

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27 August 2018

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Genome reannotation of the lizard Anolis carolinensis based on 14 adult and embryonic deep transcriptomes

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27 August 2018

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27 August 2018

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Computational identification and functional predictions of long noncoding RNA in Zea mays

27 August 2018

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Genome sequence of the oleaginous red yeast Rhodosporidium toruloides MTCC 457.

27 August 2018

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The iPlant Collaborative: Cyberinfrastructure for Plant Biology

27 August 2018

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A beginner's guide to eukaryotic genome annotation

27 August 2018

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

27 August 2018

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27 August 2018

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27 August 2018

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

27 August 2018

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Evolutionary origins of Brassicaceae specific genes in Arabidopsis thaliana.

27 August 2018

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Phylogenetic comparison of F-Box (FBX) gene superfamily within the plant kingdom reveals divergent evolutionary histories indicative of genomic drift

27 August 2018

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MITE-Hunter: a program for discovering miniature inverted-repeat transposable elements from genomic sequences

27 August 2018

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Comparative genomics reveals conservative evolution of the xylem transcriptome in vascular plants

27 August 2018

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Comparative analyses reveal distinct sets of lineage-specific genes within Arabidopsis thaliana

27 August 2018

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The B73 Maize Genome: Complexity, Diversity, and Dynamics

27 August 2018

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Identifying repeats and transposable elements in sequenced genomes: how to find your way through the dense forest of programs.

27 August 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3912085

Fine-grained annotation and classification of de novo predicted LTR retrotransposons.

27 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3912085

Evolutionary and expression signatures of pseudogenes in Arabidopsis and rice

27 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3912085

Identification and characterization of pseudogenes in the rice gene complement

27 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3912085

Expansion mechanisms and functional annotations of hypothetical genes in the rice genome

27 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3912085

Genome-wide identification of lineage-specific genes in Arabidopsis, Oryza and Populus.

27 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3912085

Infernal 1.0: inference of RNA alignments

27 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3912085

Quantitative measures for the management and comparison of annotated genomes

27 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3912085

Rfam: updates to the RNA families database

27 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3912085

REGIA, an EU project on functional genomics of transcription factors from Arabidopsis Thaliana

27 August 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3912085

Identification of novel and candidate miRNAs in rice by high throughput sequencing

27 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3912085

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

27 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3912085

LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons

27 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3912085

Database resources of the National Center for Biotechnology Information

27 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3912085

MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes

27 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3912085

Identification and characterization of lineage-specific genes within the Poaceae

27 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3912085

A large number of novel coding small open reading frames in the intergenic regions of the Arabidopsis thaliana genome are transcribed and/or under purifying selection

27 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3912085

High-throughput sequencing of Arabidopsis microRNAs: evidence for frequent birth and death of MIRNA genes

27 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3912085

EGASP: the human ENCODE Genome Annotation Assessment Project

27 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3912085

Transposable elements, gene creation and genome rearrangement in flowering plants

27 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3912085

Repbase Update, a database of eukaryotic repetitive elements

27 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3912085

InterProScan: protein domains identifier

27 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3912085

Gene finding in novel genomes

27 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3912085

Empirical analysis of transcriptional activity in the Arabidopsis genome

27 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3912085

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

27 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3912085

Plant transposable elements: where genetics meets genomics

27 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3912085

Functional annotation of a full-length Arabidopsis cDNA collection

27 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3912085

Initial sequencing and analysis of the human genome

27 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3912085

The Sequence of the Human Genome

27 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3912085

Analysis of the genome sequence of the flowering plant Arabidopsis thaliana

27 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3912085

A computational screen for methylation guide snoRNAs in yeast

27 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3912085

tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence

27 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3912085

The construction of Arabidopsis expressed sequence tag assemblies. A new resource to facilitate gene identification

27 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3912085

27 August 2018

Identifiers

DOI

10.1104/PP.113.230144

1 reference

3 December 2017

0 references

1 reference