From: Jason S. <ja...@bi...> - 2009-03-12 13:28:02
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> As an example a popular program is called maq to align Illumina > reads to a reference sequence. A useful visualization is its > 'pileup' output which shows a vertical output with the reference > sequence, orientation of reads and base changes. In my experience > Maqviewer doesn't seem to work on some of the systems I tried (due > to some GTK issues) and reports from people that have got it working > say its pretty basic. I run a core group and getting things running > on everyone's desktops (which usually means in a browser) saves > everyone's time... > Tools like EagleView from the MarthLab http://bioinformatics.bc.edu/marthlab/EagleView are really appropriate for this too. > In addition an alignment display would be useful for viewing > conservation across species at the base pair level and is already > part of the UCSC browser. The per base conservation can come from wiggle-style plotting I would think is already a good way to solve this. > > Maybe the back end could use SAM/BAM format to store the alignments http://samtools.sourceforge.net/ > which appears to be a useful emerging standard. Note there is a > ASCII viewer as part of the package > which I'll check out. > > Steve > ------------------------------------------------------------------ > Medical Sciences Division > Weatherall Institute of Molecular Medicine/Sir William Dunn School > Oxford University > > > ------------------------------------------------------------------------------ > Apps built with the Adobe(R) Flex(R) framework and Flex Builder(TM) > are > powering Web 2.0 with engaging, cross-platform capabilities. Quickly > and > easily build your RIAs with Flex Builder, the Eclipse(TM)based > development > software that enables intelligent coding and step-through debugging. > Download the free 60 day trial. http://p.sf.net/sfu/www-adobe-com > _______________________________________________ > Gmod-ajax mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-ajax Jason Stajich ja...@bi... |