(Q34031529)

30 July 2017

title

A beginner's guide to eukaryotic genome annotation (English)

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30 July 2017

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Mark Yandell

1

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30 July 2017

Daniel Ence

series ordinal

2

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30 July 2017

publication date

18 April 2012

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30 July 2017

published in

Nature Reviews Genetics

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30 July 2017

volume

13

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30 July 2017

issue

5

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30 July 2017

page(s)

329-342

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The genome sequence of Drosophila melanogaster

30 July 2017

cites work

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Direct RNA sequencing

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

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A vertebrate case study of the quality of assemblies derived from next-generation sequences

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ABACAS: algorithm-based automatic contiguation of assembled sequences

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A novel class of SINE elements derived from 5S rRNA.

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Automated characterization of potentially active retroid agents in the human genome

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Automated de novo identification of repeat sequence families in sequenced genomes

21 January 2018

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De novo identification of repeat families in large genomes

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WindowMasker: window-based masker for sequenced genomes

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Discovering and detecting transposable elements in genome sequences

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The impact of retrotransposons on human genome evolution

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Alu repeats increase local recombination rates

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Basic local alignment search tool

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BLAST+: architecture and applications

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Swiss-Prot: juggling between evolution and stability

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Protein variety and functional diversity: Swiss-Prot annotation in its biological context

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Ongoing and future developments at the Universal Protein Resource

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Database resources of the National Center for Biotechnology Information

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Automated generation of heuristics for biological sequence comparison

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Splign: algorithms for computing spliced alignments with identification of paralogs

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

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Computational methods for transcriptome annotation and quantification using RNA-seq

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ABySS: a parallel assembler for short read sequence data

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De novo assembly of human genomes with massively parallel short read sequencing

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

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TopHat: discovering splice junctions with RNA-Seq

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Fast and SNP-tolerant detection of complex variants and splicing in short reads

21 January 2018

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Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs

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Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

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Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

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Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies

21 January 2018

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Prediction of gene structure

21 January 2018

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Prediction of complete gene structures in human genomic DNA

21 January 2018

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Genie--gene finding in Drosophila melanogaster

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Genome annotation past, present, and future: how to define an ORF at each locus

21 January 2018

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Gene finding in novel genomes

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nGASP--the nematode genome annotation assessment project

21 January 2018

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EGASP: collaboration through competition to find human genes

21 January 2018

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

21 January 2018

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

21 January 2018

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GeneMark.hmm: new solutions for gene finding

21 January 2018

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Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training

21 January 2018

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Ab initio gene identification in metagenomic sequences

21 January 2018

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Integrating genomic homology into gene structure prediction.

21 January 2018

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Ab initio gene finding in Drosophila genomic DNA

21 January 2018

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GAZE: a generic framework for the integration of gene-prediction data by dynamic programming

21 January 2018

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An integrated computational pipeline and database to support whole-genome sequence annotation

21 January 2018

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Annotation of the Drosophila melanogaster euchromatic genome: a systematic review

21 January 2018

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A computational and experimental approach to validating annotations and gene predictions in the Drosophila melanogaster genome

21 January 2018

1 reference

JIGSAW: integration of multiple sources of evidence for gene prediction

21 January 2018

1 reference

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

21 January 2018

1 reference

Creating a honey bee consensus gene set

21 January 2018

1 reference

Evigan: a hidden variable model for integrating gene evidence for eukaryotic gene prediction.

21 January 2018

1 reference

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

21 January 2018

1 reference

Improved tools for biological sequence comparison

21 January 2018

1 reference

The Sequence Ontology: a tool for the unification of genome annotations

21 January 2018

1 reference

JBrowse: a next-generation genome browser

21 January 2018

1 reference

The Bioperl toolkit: Perl modules for the life sciences

21 January 2018

1 reference

Solving the Problem: Genome Annotation Standards before the Data Deluge

21 January 2018

1 reference

Towards Viral Genome Annotation Standards, Report from the 2010 NCBI Annotation Workshop

21 January 2018

1 reference

Meeting report: a workshop on Best Practices in Genome Annotation

21 January 2018

1 reference

InterPro and InterProScan: tools for protein sequence classification and comparison

21 January 2018

1 reference

The Pfam protein families database

21 January 2018

1 reference

Quantitative measures for the management and comparison of annotated genomes

21 January 2018

1 reference

Apollo: a sequence annotation editor

21 January 2018

1 reference

Artemis: sequence visualization and annotation

21 January 2018

1 reference

Fly meets shotgun: shotgun wins.

21 January 2018

1 reference

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

21 January 2018

1 reference

Hymenoptera Genome Database: integrated community resources for insect species of the order Hymenoptera

21 January 2018

1 reference

Draft genome of the globally widespread and invasive Argentine ant (Linepithema humile)

21 January 2018

1 reference

The genome sequence of the leaf-cutter ant Atta cephalotes reveals insights into its obligate symbiotic lifestyle

21 January 2018

1 reference

The genome of the leaf-cutting ant Acromyrmex echinatior suggests key adaptations to advanced social life and fungus farming.

21 January 2018

1 reference

The Ensembl automatic gene annotation system

21 January 2018

1 reference

Gramene database in 2010: updates and extensions

21 January 2018

1 reference

PlantGDB: a resource for comparative plant genomics

21 January 2018

1 reference

Phytozome: a comparative platform for green plant genomics

21 January 2018

1 reference

VectorBase: a data resource for invertebrate vector genomics

21 January 2018

1 reference

Pseudogene.org: a comprehensive database and comparison platform for pseudogene annotation

21 January 2018

1 reference

Integrated pseudogene annotation for human chromosome 22: evidence for transcription

21 January 2018

1 reference

Rfam: an RNA family database

21 January 2018

1 reference

RNAmmer: consistent and rapid annotation of ribosomal RNA genes

21 January 2018

1 reference

Plant DNA flow cytometry and estimation of nuclear genome size

21 January 2018

1 reference

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

21 January 2018

1 reference

The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs

21 January 2018

1 reference

Prediction of mammalian microRNA targets

21 January 2018

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A memory-efficient dynamic programming algorithm for optimal alignment of a sequence to an RNA secondary structure

21 January 2018

1 reference

Real-time quantification of microRNAs by stem-loop RT-PCR

21 January 2018

1 reference

Long non-coding RNAs: Guardians of development

21 January 2018

1 reference

Long noncoding RNA in genome regulation: prospects and mechanisms

21 January 2018

1 reference

Pseudogene-derived small interfering RNAs regulate gene expression in mouse oocytes

21 January 2018

1 reference

Comparative analysis of processed pseudogenes in the mouse and human genomes

21 January 2018

1 reference

Infernal 1.0: inference of RNA alignments

21 January 2018

1 reference

Evaluation of gene structure prediction programs.

21 January 2018

1 reference

Assessing the accuracy of prediction algorithms for classification: an overview

21 January 2018

1 reference

EGASP: the human ENCODE Genome Annotation Assessment Project

21 January 2018

1 reference

mGene: accurate SVM-based gene finding with an application to nematode genomes

21 January 2018

1 reference

21 January 2018

1 reference

Computational inference of homologous gene structures in the human genome

21 January 2018

1 reference

Conrad: gene prediction using conditional random fields.

21 January 2018

1 reference

CONTRAST: a discriminative, phylogeny-free approach to multiple informant de novo gene prediction

21 January 2018

1 reference

Global discriminative learning for higher-accuracy computational gene prediction

21 January 2018

1 reference

MapSplice: accurate mapping of RNA-seq reads for splice junction discovery.

21 January 2018

1 reference

Integrative genomics viewer

21 January 2018

1 reference

Repetitive DNA and next-generation sequencing: computational challenges and solutions

21 January 2018

1 reference

BLAT—The BLAST-Like Alignment Tool

31 March 2020

1 reference

Spidey: a tool for mRNA-to-genomic alignments

31 March 2020

1 reference

Optimal spliced alignment of homologous cDNA to a genomic DNA template

31 March 2020

1 reference

Molecular characterization of the Drosophila genome

31 March 2020

1 reference

12 December 2020

Using the Generic Genome Browser (GBrowse).

1 reference

12 December 2020

Pairwise RNA structure comparison with stochastic context-free grammars.

1 reference

12 December 2020

The prediction of human exons by oligonucleotide composition and discriminant analysis of spliceable open reading frames

1 reference

12 December 2020

Identifiers

DOI

10.1038/NRG3174

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Dimensions Publication ID

30 July 2017

1011134120

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