FastAlign.pl

FastAlign.pl provides a more intuitive output to find exon-intron junctions. The query string is in amino acids and the hit string is in nucleotides. There are extra nucleotides at the end of the hit string (option -diff and by default = 10), that allow to verify if the intron start with common rules (5'-GTGCGA-... for group II intron and after an exonic T for group I intron).

If you have Emboss, you can genarate a graphic with option -graph 1.

Dependencies:
- Perl
- Bioperl
- UNIX system
- tfasty
- Emboss (if you want a graphic)