I have the following problem: I aligned all available cDNA versions of a certain gene in clustalW or Mega5. It is obvious that different exons are spliced together to form similar domains in the final protein. I want to highlight this fact. Therefore I search for each exon and want to highlight it in the cDNA by a color code so I can see in which splice variant which part of the protein was combined by which exons. Unfortunately the alignment programs I use (Bioedit, MEGA5) don't allow to manually highlight sequences. If I export the file as rtf format I loose the alignment properties. If I export as a fasta I still have the alignment information but in text editor I cannot highlight with colors. I can export to excel, but there each nucleotide is in a single cell and I loose the ability to search for a certain exon sequence.
I hope somebody knows a program or an approach. Thanx