Hello,

I am looking at a bunch of standalone genome browsers / annotation editors. I am having trouble finding something which can:

• load 800Mbp draft sequence
• read gff files from few gene predictors /blast matches
• load RNA-Seq next gen mapping data
• will let me compare genome slices with these from other species
• editing annotations (splitting/merging genes)
• tagging, i.e. "confirmed_gene", "pseudogene"

So far only Artemis and Apollo have more extensive editing annotation capability. Argo and IGB/GenViz should have some basic editing (i.e delete feature) but do not seem to be concentrating on that function.

Hence my question: is there anything out there which you can recommend, or at least you have tried?

EDIT: There are two other tools used for manual annotation:

• Manatee (http://manatee.sourceforge.net/) which was mostly used for prokariotic annot.
• Otterlace custom made annotation system @Sanger (not available?)

Next release of Argo (Argo2) is one probably to watch.

Also: loading and indexing that much data in a text form does not make sense to do at the startup time (loading time 20mins + of FASTA alone). Precomputing/converting the data and loading it into a database looks like a must have feature.