Literature DB >> 36008656

How to Use the Candida Genome Database.

Marek S Skrzypek1, Jonathan Binkley1, Gavin Sherlock2.   

Abstract

The Candida Genome Database provides access to biological information about genes and proteins of several medically important Candida species. The website is organized into easily navigable pages that enable data retrieval and analysis. This chapter shows how to explore the CGD Home page and Locus Summary pages, which are the main access points to the database. It also provides a description of how to use the GO analysis tools, GO Term Finder, and GO Slim Mapper and how to browse large-scale datasets using the JBrowse genome browser. Finally, it shows how to search and retrieve data for user-defined sets of genes using the Advanced Search and Batch Download tools.
© 2022. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.

Entities:  

Keywords:  Candida; Expression analysis; GO Slim; Gene ontology; Genome database; JBrowse

Mesh：

Year:  2022        PMID： 36008656     DOI： 10.1007/978-1-0716-2549-1_4

Source DB:  PubMed          Journal:  Methods Mol Biol        ISSN： 1064-3745


  11 in total

1.  GO::TermFinder--open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes.

Authors:  Elizabeth I Boyle; Shuai Weng; Jeremy Gollub; Heng Jin; David Botstein; J Michael Cherry; Gavin Sherlock
Journal:  Bioinformatics       Date:  2004-08-05       Impact factor: 6.937

Review 2.  Biocuration at the Saccharomyces genome database.

Authors:  Marek S Skrzypek; Robert S Nash
Journal:  Genesis       Date:  2015-07-03       Impact factor: 2.487

3.  Simultaneous Emergence of Multidrug-Resistant Candida auris on 3 Continents Confirmed by Whole-Genome Sequencing and Epidemiological Analyses.

Authors:  Shawn R Lockhart; Kizee A Etienne; Snigdha Vallabhaneni; Joveria Farooqi; Anuradha Chowdhary; Nelesh P Govender; Arnaldo Lopes Colombo; Belinda Calvo; Christina A Cuomo; Christopher A Desjardins; Elizabeth L Berkow; Mariana Castanheira; Rindidzani E Magobo; Kauser Jabeen; Rana J Asghar; Jacques F Meis; Brendan Jackson; Tom Chiller; Anastasia P Litvintseva
Journal:  Clin Infect Dis       Date:  2016-10-20       Impact factor: 9.079

4.  Analysis of gene evolution and metabolic pathways using the Candida Gene Order Browser.

Authors:  David A Fitzpatrick; Peadar O'Gaora; Kevin P Byrne; Geraldine Butler
Journal:  BMC Genomics       Date:  2010-05-10       Impact factor: 3.969

5.  The diploid genome sequence of Candida albicans.

Authors:  Ted Jones; Nancy A Federspiel; Hiroji Chibana; Jan Dungan; Sue Kalman; B B Magee; George Newport; Yvonne R Thorstenson; Nina Agabian; P T Magee; Ronald W Davis; Stewart Scherer
Journal:  Proc Natl Acad Sci U S A       Date:  2004-05-03       Impact factor: 11.205

6.  The Candida genome database incorporates multiple Candida species: multispecies search and analysis tools with curated gene and protein information for Candida albicans and Candida glabrata.

Authors:  Diane O Inglis; Martha B Arnaud; Jonathan Binkley; Prachi Shah; Marek S Skrzypek; Farrell Wymore; Gail Binkley; Stuart R Miyasato; Matt Simison; Gavin Sherlock
Journal:  Nucleic Acids Res       Date:  2011-11-07       Impact factor: 16.971

7.  The Candida Genome Database (CGD): incorporation of Assembly 22, systematic identifiers and visualization of high throughput sequencing data.

Authors:  Marek S Skrzypek; Jonathan Binkley; Gail Binkley; Stuart R Miyasato; Matt Simison; Gavin Sherlock
Journal:  Nucleic Acids Res       Date:  2016-10-13       Impact factor: 16.971

8.  Saccharomyces Genome Database provides mutant phenotype data.

Authors:  Stacia R Engel; Rama Balakrishnan; Gail Binkley; Karen R Christie; Maria C Costanzo; Selina S Dwight; Dianna G Fisk; Jodi E Hirschman; Benjamin C Hitz; Eurie L Hong; Cynthia J Krieger; Michael S Livstone; Stuart R Miyasato; Robert Nash; Rose Oughtred; Julie Park; Marek S Skrzypek; Shuai Weng; Edith D Wong; Kara Dolinski; David Botstein; J Michael Cherry
Journal:  Nucleic Acids Res       Date:  2009-11-11       Impact factor: 16.971

9.  Evolution of pathogenicity and sexual reproduction in eight Candida genomes.

Authors:  Geraldine Butler; Matthew D Rasmussen; Michael F Lin; Manuel A S Santos; Sharadha Sakthikumar; Carol A Munro; Esther Rheinbay; Manfred Grabherr; Anja Forche; Jennifer L Reedy; Ino Agrafioti; Martha B Arnaud; Steven Bates; Alistair J P Brown; Sascha Brunke; Maria C Costanzo; David A Fitzpatrick; Piet W J de Groot; David Harris; Lois L Hoyer; Bernhard Hube; Frans M Klis; Chinnappa Kodira; Nicola Lennard; Mary E Logue; Ronny Martin; Aaron M Neiman; Elissavet Nikolaou; Michael A Quail; Janet Quinn; Maria C Santos; Florian F Schmitzberger; Gavin Sherlock; Prachi Shah; Kevin A T Silverstein; Marek S Skrzypek; David Soll; Rodney Staggs; Ian Stansfield; Michael P H Stumpf; Peter E Sudbery; Thyagarajan Srikantha; Qiandong Zeng; Judith Berman; Matthew Berriman; Joseph Heitman; Neil A R Gow; Michael C Lorenz; Bruce W Birren; Manolis Kellis; Christina A Cuomo
Journal:  Nature       Date:  2009-06-04       Impact factor: 49.962

10.  Comparative genome analysis and gene finding in Candida species using CGOB.

Authors:  Sarah L Maguire; Seán S ÓhÉigeartaigh; Kevin P Byrne; Markus S Schröder; Peadar O'Gaora; Kenneth H Wolfe; Geraldine Butler
Journal:  Mol Biol Evol       Date:  2013-03-13       Impact factor: 16.240
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