Artemis, Apollo Or Anything For Genome Annotation Editing With Next Gen Sequence Data

Question

[Darked89]

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.

[Nicojo]

I've mainly been using Artemis, which I like a lot. But I don't have as many needs as you do ;)

Answer 1

[Yannick Wurm]

We've been using Apollo... it has many features & offers a great overview of what types of evidence you have for your genes. And it can open many different file formats & remote databaes. But there still is clearly still a lot of potential.

For example it seems like it should be trivial for a non-computational person to provide an additional source of evidence (eg: the cDNA they just sequenced in the lab to help choose between two potential gene models). But afaik thats impossible.

Maybe Apple or Google should make a genome annotation tool :)

Answer 2

[Louis Letourneau]

We've been using artemis to annotate our bacterial genome. Nothing in the 100Mb+ range, more 1-10Mb.

It worked very well for this. I would guess it would work for your dataset(s) if you have a massive(memory-wise) desktop to run it.

[User 59]

Artemis, venerable but still useful, we use it too.