Literature DB >> 22956109

On-line resources for Xenopus.

Jeff Bowes1.   

Abstract

Since the advent of computational methods in biology, the quantity of biological data has grown exponentially. These data support genomic, genetic, developmental, and other forms of biological experimentation. The number of on-line resources has kept pace with the growth in data. Xenopus has perhaps lagged some of the other model organisms in developing resources, but is now quickly catching up. There are now a number of well-established and developing resources for Xenopus. This chapter looks beyond the widely known public databases, Genbank and the EBI, and describes how the researcher can use a number of central sites such as Xenbase, UniProtKB, and major genome browsers to navigate to a variety of different resources.

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Year:  2012        PMID: 22956109      PMCID: PMC4300944          DOI: 10.1007/978-1-61779-992-1_31

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


  28 in total

1.  Using the Generic Genome Browser (GBrowse).

Authors:  Maureen J Donlin
Journal:  Curr Protoc Bioinformatics       Date:  2009-12

2.  The genome of the Western clawed frog Xenopus tropicalis.

Authors:  Uffe Hellsten; Richard M Harland; Michael J Gilchrist; David Hendrix; Jerzy Jurka; Vladimir Kapitonov; Ivan Ovcharenko; Nicholas H Putnam; Shengqiang Shu; Leila Taher; Ira L Blitz; Bruce Blumberg; Darwin S Dichmann; Inna Dubchak; Enrique Amaya; John C Detter; Russell Fletcher; Daniela S Gerhard; David Goodstein; Tina Graves; Igor V Grigoriev; Jane Grimwood; Takeshi Kawashima; Erika Lindquist; Susan M Lucas; Paul E Mead; Therese Mitros; Hajime Ogino; Yuko Ohta; Alexander V Poliakov; Nicolas Pollet; Jacques Robert; Asaf Salamov; Amy K Sater; Jeremy Schmutz; Astrid Terry; Peter D Vize; Wesley C Warren; Dan Wells; Andrea Wills; Richard K Wilson; Lyle B Zimmerman; Aaron M Zorn; Robert Grainger; Timothy Grammer; Mustafa K Khokha; Paul M Richardson; Daniel S Rokhsar
Journal:  Science       Date:  2010-04-30       Impact factor: 47.728

3.  The Pfam protein families database.

Authors:  Robert D Finn; Jaina Mistry; John Tate; Penny Coggill; Andreas Heger; Joanne E Pollington; O Luke Gavin; Prasad Gunasekaran; Goran Ceric; Kristoffer Forslund; Liisa Holm; Erik L L Sonnhammer; Sean R Eddy; Alex Bateman
Journal:  Nucleic Acids Res       Date:  2009-11-17       Impact factor: 16.971

4.  Genomicus: a database and a browser to study gene synteny in modern and ancestral genomes.

Authors:  Matthieu Muffato; Alexandra Louis; Charles-Edouard Poisnel; Hugues Roest Crollius
Journal:  Bioinformatics       Date:  2010-02-24       Impact factor: 6.937

5.  The Comparative Toxicogenomics Database: update 2011.

Authors:  Allan Peter Davis; Benjamin L King; Susan Mockus; Cynthia G Murphy; Cynthia Saraceni-Richards; Michael Rosenstein; Thomas Wiegers; Carolyn J Mattingly
Journal:  Nucleic Acids Res       Date:  2010-09-22       Impact factor: 16.971

6.  The UCSC Genome Browser database: update 2011.

Authors:  Pauline A Fujita; Brooke Rhead; Ann S Zweig; Angie S Hinrichs; Donna Karolchik; Melissa S Cline; Mary Goldman; Galt P Barber; Hiram Clawson; Antonio Coelho; Mark Diekhans; Timothy R Dreszer; Belinda M Giardine; Rachel A Harte; Jennifer Hillman-Jackson; Fan Hsu; Vanessa Kirkup; Robert M Kuhn; Katrina Learned; Chin H Li; Laurence R Meyer; Andy Pohl; Brian J Raney; Kate R Rosenbloom; Kayla E Smith; David Haussler; W James Kent
Journal:  Nucleic Acids Res       Date:  2010-10-18       Impact factor: 16.971

7.  The European Bioinformatics Institute's data resources.

Authors:  Catherine Brooksbank; Graham Cameron; Janet Thornton
Journal:  Nucleic Acids Res       Date:  2009-11-24       Impact factor: 16.971

8.  Xenbase: gene expression and improved integration.

Authors:  Jeff B Bowes; Kevin A Snyder; Erik Segerdell; Chris J Jarabek; Kenan Azam; Aaron M Zorn; Peter D Vize
Journal:  Nucleic Acids Res       Date:  2009-11-01       Impact factor: 16.971

9.  BioMart--biological queries made easy.

Authors:  Damian Smedley; Syed Haider; Benoit Ballester; Richard Holland; Darin London; Gudmundur Thorisson; Arek Kasprzyk
Journal:  BMC Genomics       Date:  2009-01-14       Impact factor: 3.969

10.  Rfam: updates to the RNA families database.

Authors:  Paul P Gardner; Jennifer Daub; John G Tate; Eric P Nawrocki; Diana L Kolbe; Stinus Lindgreen; Adam C Wilkinson; Robert D Finn; Sam Griffiths-Jones; Sean R Eddy; Alex Bateman
Journal:  Nucleic Acids Res       Date:  2008-10-25       Impact factor: 16.971

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