Gene prediction and genome assembly

Question

[murali]

Is there any siginficant correlation between de novo genome assembly followed by gene prediction?

Is there a possibility to compare both of them?

[al.bodrug]

Even if it does not inform you directly of the quality of the assembly, the number of genes found in the assembly indicates that what you have is a biologically possible molecule. That means that even if your assembly contigs are not exact, they are plausible. However if you don't find all or most expected genes, you can throw your contigs away.

You can compare your assembly metrics (N50, largest contig) with the number of genes you are able to indentify in your assembly. Quast does both. Mitofy is a gene prediction tool specific to mitochondries. I'm sure there are more.

[Phil S.]

Can you please be more specific in your question. de novo genome assembly is a completly differnt thing than gene prediction..

Answer 1

[HG]

After assembly you can check your assembly quality and Gene prediction by Quast. If assembly is good then you can find near about equal number of gene with reference genome.

http://sourceforge.net/projects/quast/files/