3.3.8 Confrontation with Genome Annotation

With VAMP it is possible to compare a molecular profile with genome annotations, for example gene structure: the user can load a pseudo-profile with the structure of all known genes (introns, exons, splicing variants). Several functions are offered. Proceed as follows:

• import the genome annotation data (see Figures 3.55)
• put a landmark on your favorite gene and center on it (see Figures 3.56)

Figure 3.55: File $\rightarrow$ Import - Start by importing genome annotation data.

Figure 3.56: Genome Annotation - Then you can put a landmark on your favorite gene and center on it.

Then you can zoom on the landmark until the gene structure is visible (see Figures 3.57).

Figure 3.57: Genome Annotation (zoom 3x)

Right-clicking brings up a menu which allows to open web pages from NCBI gene, UCSC Genome Browser or Ensembl ContigView (see Figures 3.58).

Figure 3.58: Genome Annotation (zoom 30x) (exons in red, introns in yellow, UTR 3' in light green and UTR 5' in dark green)