[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.

[bioinfosm]

sorry, but whats DIP?

[steven]

i bet on deletion insertion polymorphism.

[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.

[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]

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.

[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]

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.