GenePalette: a universal software tool for genome sequence visualization and analysis

Developmental Biology
Mark Rebeiz, J W Posakony

Abstract

To make effective use of the growing host of complete genome sequences, biologists must have easy-to-use software tools that allow them to visualize, analyze, and modify genome data in an interactive and generalized manner. In an effort to bridge the gap between genome and researcher, we have created GenePalette (www.genepalette.org), a desktop application that can access any genome sequence and display the positions of various features [e.g., transcription factor binding sites (TFBSs)] relative to the introns and exons of annotated genes. Written in Java, GenePalette can run on all Java-supporting operating systems (Mac, PC, Unix, Linux). Annotated sequence encompassing the majority of public genome data is rapidly retrieved from GenBank or Ensembl. The software provides intuitive access to the selected genomic region through three interface components: a colorful graphical display showing a schematic of genes and features; an annotated sequence view in which features and genes are highlighted directly on the sequence; and the selectable raw sequence. The three interface components are fully integrated and presented on one page, permitting the user to move easily between representations at different levels of resolution, rangi...Continue Reading

References

Jan 10, 2003·Nucleic Acids Research·D KarolchikUNKNOWN University of California Santa Cruz
Jan 10, 2003·Nucleic Acids Research·V MatysE Wingender
Apr 16, 2003·Nature·Francis S CollinsUNKNOWN US National Human Genome Research Institute
Dec 19, 2003·Nucleic Acids Research·Dennis A BensonDavid L Wheeler
Dec 19, 2003·Nucleic Acids Research·David L WheelerLukas Wagner
Dec 19, 2003·Nucleic Acids Research·E BirneyT Hubbard

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Citations

Sep 2, 2009·Briefings in Bioinformatics·Jerome SalseCatherine Feuillet
Aug 16, 2006·Proceedings of the National Academy of Sciences of the United States of America·Frédéric BiemarMichael S Levine
Aug 2, 2006·Molecular and Cellular Biology·Timothy J ParnellPamela K Geyer
Jan 27, 2009·Proceedings of the National Academy of Sciences of the United States of America·Joseph C PearsonWilliam McGinnis
Jul 19, 2005·Development Genes and Evolution·Peter W Osborne, Peter K Dearden
Jul 18, 2009·The Journal of Heredity·Kathryn B WaltersDiana L E Johnson
May 10, 2013·Bioinformatics·Joseph C Pearson, Stephen T Crews
Nov 13, 2013·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Andrea I Ramos, Scott Barolo
Jun 3, 2015·Proceedings of the National Academy of Sciences of the United States of America·Shigeyuki KoshikawaSean B Carroll
Nov 6, 2008·Molecular and Cellular Endocrinology·Ann M TarrantJerzy Adamski
Dec 22, 2011·Developmental Biology·Mark RebeizJames W Posakony
Mar 2, 2005·Developmental Cell·Nick Reeves, James W Posakony
Feb 24, 2015·Developmental Biology·Enrica CharbonnierGeorge Pyrowolakis
May 24, 2014·Developmental Biology·Joseph C Pearson, Stephen T Crews
May 17, 2005·Developmental Biology·Mark RebeizJames W Posakony
Dec 1, 2012·Proceedings of the National Academy of Sciences of the United States of America·Nicolás FrankelDavid L Stern
Apr 15, 2017·American Journal of Physiology. Gastrointestinal and Liver Physiology·Asma Al MenhaliLinda C Samuelson
Feb 4, 2009·Applied Biochemistry and Biotechnology·Alok Malaviya, James Gomes
Apr 9, 2010·Nature·Thomas WernerSean B Carroll

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