[pedrotanno]

Using Arthemis we can import the annotations, but using CLC and the same GFF annotation file we can't.
The problem using Artemis is that we are having problem extracting the snps annotations in CLC... so in one program we have the exon annotations and in CLC we have our snps annotations.

[NextGenSeq]

Note CLC Bio will import the reference genome file from GenBank with the annotations. The files get very large if you include all the annotations. However, for small genomes it can handle all the annotations.

[pedrotanno]

We are trying to know where the coding exons and SNPs are, to see if our snps are on coding regions.
We tried to import one annotated reference genome and only the annotation file (GFF) but none of this approaches worked.

[zee]

If you're looking to do basic analysis have a look at some open solutions e.g. DIYA. It's quite simple to run a set of programs in serial. The hard part with annotation is manual curation and Artemis is a good tried and tested option. Geneious has some good offerings and it is prettier.

[pedrotanno]

CLC Bio is a bit buggy. You have to force import your reference genome as normal sequence data NOT next gen sequence data. Once you do that it is easy to annotate it using a GFF file. I tried attach the pdf describing it but this website gave an error message. If you private message me with your email address I can email it to you.

Hi guys,
I'm having the same problem using CLC ... and I couldn't find any viable solution...About this pdf... is it from Clc? Because not even using their example data from the 'Annotation Plug-in' we could make it work.

[steven]

i bet on deletion insertion polymorphism.

[bioinfosm]

sorry, but whats DIP?

[steven]

You have to annotate your reference genome to know where the coding exons and SNPs are. After the assembly and SNP/DIP detection the software tells you if the variations are coding or known SNPs. You have to know this for mutation discovery.

OK, so that is not "gene prediction" as mentioned in the first post -if i get it right. If you want to automatically annotated gene structures on a genomic sequence, then look for something like G-Morse or Cufflink, or a traditional gene finder.

[NextGenSeq]

You have to annotate your reference genome to know where the coding exons and SNPs are. After the assembly and SNP/DIP detection the software tells you if the variations are coding or known SNPs. You have to know this for mutation discovery.

[steven]

I have the same question than husamia: what do you mean by "annotate"?
Labeling a genomic region as a "contig/cluster/whatever of reads/ESTs/whatever" is one thing, performing automatic gene structure prediction is a totally different exercice (although both can produce a GFF file). I do not believe that CLC nor Geneious do the latter.

[johnny]

When you mark a base you can right-click on it and use the "Add Annotation".
For extracting annotations you have to install a plugin called "Extract annotations"

http://www.clcbio.com/index.php?id=873

There you also find the "Annotate Sequence with GFF File" plugin.

[NextGenSeq]

CLC Bio is a bit buggy. You have to force import your reference genome as normal sequence data NOT next gen sequence data. Once you do that it is easy to annotate it using a GFF file. I tried attach the pdf describing it but this website gave an error message. If you private message me with your email address I can email it to you.

[alpapan]

alternatively

Hey

We've been using Geneious Pro rather successfully to accomplish this for small contigs (I guess it depends how much memory your computer has). It allows to annotate a sequence, export it as GFF. You can also import other GFFs as annotations only (i.e. if it is a GFF file without a FASTA section but you have a geneious document with the reference sequence).

Geneious is also prettier than CLC bio and much much cheaper...

cheers,
a

[Anelda]

You did pay for the software so support is obligatory

That's just the thing. Haven't bought it yet. Still trying to determine what percentage of our work could be done on it. Have the trial version. The vendor has been helpful, but not really answering my question so far. That's why I've gone to the community in the meanwhile. Will poke the vendor again today.

[KevinLam]

Oh no worries, just wanted to clarify the problem in case I am misunderstanding the question.
I would think that commercial providers would be able to help your question better?
You might get an answer here but I would think getting info from the source would be much more directed and helpful?
You did pay for the software so support is obligatory