As for BLAST, there are several programs available in the FASTA suite of programs:

• fasta3: searches a DNA database with a DNA query sequence, or a protein database with a protein sequence
• fastx/y3: searches a protein database for homologs to a DNA query sequence, translated in both the forward and reverse frames
• tfastx/y3: searches a translated DNA database with a protein query sequence
• fasts3: compares linked peptides to a protein database
• fastf3 compares mixed peptides to a protein databank

There are a variety of options available on the EBI FASTA server. You can choose to get your results back by e-mail. If you choose this option (by changing the pull-down menu under the "Results" link from "interactive" to "email", then you must also fill in your e-mail address in the first text-entry box (under the "YOUR EMAIL" link). In the "Search Title" text-entry box, you may input any text by which you can identify your results. The other options can change depending on whether you have a protein or a DNA query sequence, and whether you want to search a protein or DNA database with your query. The table below summarizes these changes.

You input your query sequence into the large text-entry box. Your query sequence can be in any of the more common sequence formats (FASTA, GCG, EMBL, Genbank, NBRF, Phylip or as raw text). However, if your sequence is DNA and contains more than 50% ambiguity codes it will be rejected by the system.