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FastAlign is a perl script which uses the heuristic method of tfasty
...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)
EMBOSS is a dynamic and comprehensive Open Source package for bioinformatics (DNA and protein sequence analysis, protein structure, phylogenetics, etc.). EMBOSS is written in C, also compatible with C++, and has a separate Java interface (Jemboss)
EMBOSS explorer is a web-based graphical user interface to the EMBOSS suite of bioinformatics tools. It is written in Perl and is exceedingly simple to install, configure, maintain and use.
gbwget is a command line/screen oriented tool to search in nucleotide
or protein databases and to view or retrieve database entries.
It can easily integrated into the EMBOSS seqence analysis
Suite can also be used standalone.
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