User talk:Darek Kedra/sandbox 20

=Notes on genome browsers =

=Web based= http://genseq.molgen.mpg.de/ssRNA/
 * Parkhomchuk, Nucl Acids Res,2009

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

=Stand Alone=

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
 * Integrated Genome Browser from BROAD

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

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

available Arabidopsis annotation data via DAS from their web site

http://genoviz.sourceforge.net/ (GenoViz)
 * 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 active developement No tracs, no gene models, no editing Excelent short read viewer supporting multiple formats
 * Tablet