Gene Annotation

''The greatest wealth is to live content with little, Plato''

Today I tried to reach Taner to discuss about the next steps. He informed me that he had already done the annotation for SOAP results. However we agreed that since Abyss presents better results on scaffolds results, he should also annotate Abyss output.

So, he used exonerate in order to do the alignment first by using as reference the spruce genome chloroplast. In Exonerate you can choose from different alignment models.

Afterwards, he converted the alignment of exonerate to fasta file and he put it to dogma to do the annotation. Dogma is ideal for annotating plant chloroplast and animal mitochondrial genomes. The gen bank file he used was taken from the NCBI database.

In the end, he used the OrganellarGenomeDraw in order to visualize the circular chloroplast genome. The result was that the total genome length is 124kb with 113 genes annotated genes.