Literature DB >> 18202028

The SGN comparative map viewer.

Lukas A Mueller1, Adri A Mills, Beth Skwarecki, Robert M Buels, Naama Menda, Steven D Tanksley.   

Abstract

MOTIVATION: With the rapid accumulation of genetic data for a multitude of different species, the availability of intuitive comparative genomic tools becomes an important requirement for the research community. Here we describe a web-based comparative viewer for mapping data, including genetic, physical and cytological maps, that is part of the SGN website (http://sgn.cornell.edu/) but that can also be installed and adapted for other websites. In addition to viewing and comparing different maps stored in the SGN database, the viewer allows users to upload their own maps and compare them to other maps in the system. The viewer is implemented in object oriented Perl, with a simple extensible interface to write data adapters for other relational database schemas and flat file formats.

Mesh：

Year:  2008        PMID： 18202028     DOI： 10.1093/bioinformatics/btm597

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  17 in total

1.  A community-based annotation framework for linking solanaceae genomes with phenomes.

Authors:  Naama Menda; Robert M Buels; Isaak Tecle; Lukas A Mueller
Journal:  Plant Physiol       Date:  2008-06-06       Impact factor: 8.340

2.  Tripal MapViewer: A tool for interactive visualization and comparison of genetic maps.

Authors:  Katheryn Buble; Sook Jung; Jodi L Humann; Jing Yu; Chun-Huai Cheng; Taein Lee; Stephen P Ficklin; Heidi Hough; Bradford Condon; Margaret E Staton; Jill L Wegrzyn; Dorrie Main
Journal:  Database (Oxford)       Date:  2019-01-01       Impact factor: 3.451

3.  solQTL: a tool for QTL analysis, visualization and linking to genomes at SGN database.

Authors:  Isaak Y Tecle; Naama Menda; Robert M Buels; Esther van der Knaap; Lukas A Mueller
Journal:  BMC Bioinformatics       Date:  2010-10-21       Impact factor: 3.169

4.  Identification of single-copy orthologous genes between Physalis and Solanum lycopersicum and analysis of genetic diversity in Physalis using molecular markers.

Authors:  Jingli Wei; Xiaorong Hu; Jingjing Yang; Wencai Yang
Journal:  PLoS One       Date:  2012-11-16       Impact factor: 3.240

5.  miSolRNA: A tomato micro RNA relational database.

Authors:  Ariel A Bazzini; Ramón Asís; Virginia González; Sebastián Bassi; Mariana Conte; Marcelo Soria; Alisdair R Fernie; Sebastián Asurmendi; Fernando Carrari
Journal:  BMC Plant Biol       Date:  2010-11-08       Impact factor: 4.215

6.  Comparative visualization of genetic and physical maps with Strudel.

Authors:  Micha Bayer; Iain Milne; Gordon Stephen; Paul Shaw; Linda Cardle; Frank Wright; David Marshall
Journal:  Bioinformatics       Date:  2011-03-03       Impact factor: 6.937

7.  Genetic dissection of vitamin E biosynthesis in tomato.

Authors:  Juliana Almeida; Leandro Quadrana; Ramón Asís; Nathalia Setta; Fabiana de Godoy; Luisa Bermúdez; Santiago N Otaiza; Junia V Corrêa da Silva; Alisdair R Fernie; Fernando Carrari; Magdalena Rossi
Journal:  J Exp Bot       Date:  2011-04-28       Impact factor: 6.992

8.  CMap 1.01: a comparative mapping application for the Internet.

Authors:  Ken Youens-Clark; Ben Faga; Immanuel V Yap; Lincoln Stein; Doreen Ware
Journal:  Bioinformatics       Date:  2009-07-30       Impact factor: 6.937

9.  From manual curation to visualization of gene families and networks across Solanaceae plant species.

Authors:  Anuradha Pujar; Naama Menda; Aureliano Bombarely; Jeremy D Edwards; Susan R Strickler; Lukas A Mueller
Journal:  Database (Oxford)       Date:  2013-05-15       Impact factor: 3.451

10.  ArkMAP: integrating genomic maps across species and data sources.

Authors:  Trevor Paterson; Andy Law
Journal:  BMC Bioinformatics       Date:  2013-08-13       Impact factor: 3.169
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