Literature DB >> 25501943

Genome Annotation and Curation Using MAKER and MAKER-P.

Michael S Campbell1, Carson Holt, Barry Moore, Mark Yandell.   

Abstract

This unit describes how to use the genome annotation and curation tools MAKER and MAKER-P to annotate protein-coding and noncoding RNA genes in newly assembled genomes, update/combine legacy annotations in light of new evidence, add quality metrics to annotations from other pipelines, and map existing annotations to a new assembly. MAKER and MAKER-P can rapidly annotate genomes of any size, and scale to match available computational resources.
Copyright © 2014 John Wiley & Sons, Inc.

Entities:  

Keywords:  comparative genomics; gene finding; genome annotation; plants

Mesh：

Year:  2014        PMID： 25501943      PMCID： PMC4286374          DOI： 10.1002/0471250953.bi0411s48

Source DB:  PubMed          Journal:  Curr Protoc Bioinformatics        ISSN： 1934-3396


  23 in total

Review 1.  A beginner's guide to eukaryotic genome annotation.

Authors:  Mark Yandell; Daniel Ence
Journal:  Nat Rev Genet       Date:  2012-04-18       Impact factor: 53.242

Review 2.  Repbase Update, a database of eukaryotic repetitive elements.

Authors:  J Jurka; V V Kapitonov; A Pavlicek; P Klonowski; O Kohany; J Walichiewicz
Journal:  Cytogenet Genome Res       Date:  2005       Impact factor: 1.636

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

Authors:  T M Lowe; S R Eddy
Journal:  Nucleic Acids Res       Date:  1997-03-01       Impact factor: 16.971

4.  Rapid and sensitive protein similarity searches.

Authors:  D J Lipman; W R Pearson
Journal:  Science       Date:  1985-03-22       Impact factor: 47.728

5.  A computational screen for methylation guide snoRNAs in yeast.

Authors:  T M Lowe; S R Eddy
Journal:  Science       Date:  1999-02-19       Impact factor: 47.728

Review 6.  Genome sequence of the nematode C. elegans: a platform for investigating biology.

Authors: 
Journal:  Science       Date:  1998-12-11       Impact factor: 47.728

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

Authors:  Michael S Campbell; MeiYee Law; Carson Holt; Joshua C Stein; Gaurav D Moghe; David E Hufnagel; Jikai Lei; Rujira Achawanantakun; Dian Jiao; Carolyn J Lawrence; Doreen Ware; Shin-Han Shiu; Kevin L Childs; Yanni Sun; Ning Jiang; Mark Yandell
Journal:  Plant Physiol       Date:  2013-12-04       Impact factor: 8.340

8.  InterProScan: protein domains identifier.

Authors:  E Quevillon; V Silventoinen; S Pillai; N Harte; N Mulder; R Apweiler; R Lopez
Journal:  Nucleic Acids Res       Date:  2005-07-01       Impact factor: 16.971

9.  Unique features of the loblolly pine (Pinus taeda L.) megagenome revealed through sequence annotation.

Authors:  Jill L Wegrzyn; John D Liechty; Kristian A Stevens; Le-Shin Wu; Carol A Loopstra; Hans A Vasquez-Gross; William M Dougherty; Brian Y Lin; Jacob J Zieve; Pedro J Martínez-García; Carson Holt; Mark Yandell; Aleksey V Zimin; James A Yorke; Marc W Crepeau; Daniela Puiu; Steven L Salzberg; Pieter J Dejong; Keithanne Mockaitis; Doreen Main; Charles H Langley; David B Neale
Journal:  Genetics       Date:  2014-03       Impact factor: 4.562

10.  Gene finding in novel genomes.

Authors:  Ian Korf
Journal:  BMC Bioinformatics       Date:  2004-05-14       Impact factor: 3.169
View more
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2.  Novel proteases from the genome of the carnivorous plant Drosera capensis: Structural prediction and comparative analysis.

Authors:  Carter T Butts; Jan C Bierma; Rachel W Martin
Journal:  Proteins       Date:  2016-07-13

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4.  Host genome integration and giant virus-induced reactivation of the virophage mavirus.

Authors:  Matthias G Fischer; Thomas Hackl
Journal:  Nature       Date:  2016-12-07       Impact factor: 49.962

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Journal:  Mol Genet Genomics       Date:  2018-01-02       Impact factor: 3.291

6.  Plant evolution and environmental adaptation unveiled by long-read whole-genome sequencing of Spirodela.

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7.  Subgenome Dominance in an Interspecific Hybrid, Synthetic Allopolyploid, and a 140-Year-Old Naturally Established Neo-Allopolyploid Monkeyflower.

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Journal:  Plant Cell       Date:  2017-08-16       Impact factor: 11.277

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9.  De novo phased assembly of the Vitis riparia grape genome.

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10.  The Cyclically Seasonal Drosophila subobscura Inversion O7 Originated From Fragile Genomic Sites and Relocated Immunity and Metabolic Genes.

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