Artemis, Apollo Or Anything For Genome Annotation Editing With Next Gen Sequence Data
2
8
Entering edit mode
14.1 years ago
Darked89 4.6k

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:

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.

genome next-gen-sequencing annotation • 6.1k views
ADD COMMENT
0
Entering edit mode

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

ADD REPLY
5
Entering edit mode
13.6 years ago
Yannick Wurm ★ 2.5k

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 :)

ADD COMMENT
3
Entering edit mode
14.1 years ago

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.

ADD COMMENT
1
Entering edit mode

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

ADD REPLY

Login before adding your answer.

Traffic: 1902 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6