Does anyone know of a program that can align a genomic sequence with introns with the corresponding amino acid sequence?
I have both the genomic sequence and the correct amino acid sequence but no information on the genemodel in e.g. gff or genbank format.
This is not what one would call a 'normal' alignment, but I would like it to look like this:
nucleotide sequence with intron in italic:
corresponding amino acid sequence:
The intron does not encode for amino acid which should thus result in a gap in the 'alignment'. Desired 'alignment':
ATGCACGATACGACTGACGTACGTACGTACGTACGTACGTACGTACGGAGACGTAGACTC M H D T T D V R T Y V R R R R L