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Verdant: automated annotation, alignment and phylogenetic analysis of whole chloroplast genomes.
McKain, Michael R; Hartsock, Ryan H; Wohl, Molly M; Kellogg, Elizabeth A.
Afiliação
  • McKain MR; Donald Danforth Plant Science Center, St. Louis, MO 63132, USA.
  • Hartsock RH; Donald Danforth Plant Science Center, St. Louis, MO 63132, USA.
  • Wohl MM; Donald Danforth Plant Science Center, St. Louis, MO 63132, USA.
  • Kellogg EA; Donald Danforth Plant Science Center, St. Louis, MO 63132, USA.
Bioinformatics ; 33(1): 130-132, 2017 01 01.
Article em En | MEDLINE | ID: mdl-27634949
MOTIVATION: Chloroplast genomes are now produced in the hundreds for angiosperm phylogenetics projects, but current methods for annotation, alignment and tree estimation still require some manual intervention reducing throughput and increasing analysis time for large chloroplast systematics projects. RESULTS: Verdant is a web-based software suite and database built to take advantage a novel annotation program, annoBTD. Using annoBTD, Verdant provides accurate annotation of chloroplast genomes without manual intervention. Subsequent alignment and tree estimation can incorporate newly annotated and publically available plastomes and can accommodate a large number of taxa. Verdant sharply reduces the time required for analysis of assembled chloroplast genomes and removes the need for pipelines and software on personal hardware. AVAILABILITY AND IMPLEMENTATION: Verdant is available at: http://verdant.iplantcollaborative.org/plastidDB/ It is implemented in PHP, Perl, MySQL, Javascript, HTML and CSS with all major browsers supported. CONTACT: mrmckain@gmail.comSupplementary information: Supplementary data are available at Bioinformatics online.
Assuntos

Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Filogenia / Plantas / Software / Análise de Sequência de DNA / Bases de Dados de Ácidos Nucleicos / Genoma de Cloroplastos Idioma: En Ano de publicação: 2017 Tipo de documento: Article

Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Filogenia / Plantas / Software / Análise de Sequência de DNA / Bases de Dados de Ácidos Nucleicos / Genoma de Cloroplastos Idioma: En Ano de publicação: 2017 Tipo de documento: Article