How to align genomic sequence with corresponding amino acid sequence 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:
Hypothetical example:
nucleotide sequence with intron in italic:
ATGCACGATACGACTGACGTACGTACGTACGTACGTACGTACGTACGGAGACGTAGACTC
corresponding amino acid sequence:
MHDTTDVRTYVRRRRL
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
Have a look at exonerate's protein2genome!
From the documentation:


  Aligning a protein to genomic sequence:
  
  Similarly, it is possible to align a protein sequence to the genome, (similar to GeneWise, but with
  heuristics).
  
  exonerate --model protein2genome query.fasta target.fasta 
  
  This model will allow introns in the alignment, but also allow frameshifts, and
  exon phase changes when a codon is split by an intron.