User talk:Darek Kedra/sandbox 20

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Notes on genome browsers

Web based

  • Parkhomchuk, Nucl Acids Res,2009

http://genseq.molgen.mpg.de/ssRNA/

Procedure: viewed # 'S.cerevisiae' and 'whole brain B6' data Notes: Simple web interface, no gene info, no tracks/other annotation. opinion: SKIP

Stand Alone

  • Integrated Genome Browser from BROAD

http://www.broadinstitute.org/igv/?q=home Procedure: Downloaded and executed on bee, followed tutorial IGV User Guifde Notes: good at displaying expression data together with the genome. Multiple tracks available, but judging from tutorial it is not primarily oriented towards multiple contigs/draft assemblies. No possibility of editing annotation

developement driven by internal needs at Broad (SeqAnswers forum developer post) opinion: SKIP for time being


  • IGB and GenoViz

http://www.bioviz.org/igb/ (IGB) Procedure: Java Web Start Only (not started yet),

available Arabidopsis annotation data via DAS from their web site


  • GenoViz

http://genoviz.sourceforge.net/ (GenoViz)

Procedure: downloaded and started version 6.1 from http://sourceforge.net/projects/genoviz/files/ Java based, with a Tablet-like interface. loaded via net arabidopsis database Notes: Pros: can download annotations from remote DAS servers. Sensibly looking screen shots in user manual. ability to load gff and psl files (untested) Cons: managed to freeze whole window while investigating options

opinion: WATCH this space


EagleView: http://bioinformatics.bc.edu/marthlab/EagleView

listed as "EagleView (deprecated)" on developers web site:

  • Tablet

Tablet active developement No tracs, no gene models, no editing Excelent short read viewer supporting multiple formats