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fasta-utils is a collection of command-line utilities for editing and viewing DNA and protein sequences. All fasta* programs take input (from stdin) in FASTA format and many also produce output in FASTA format, allowing them to be chained together with pipes. Here is a list of the programs and a short description of what they do: fastacat Catenate all sequences into one sequence fastacomplement Replace each sequence with its reverse complement fastacount Report sequence length fastadigest Split sequences at restriction sites fastagap Report positions of gaps in sequences fastahead Echo only the first part of sequences fastalint Reformat sequences to standard display width fastaorf Find open reading frames fastastack Interleave sequences for 'side-by-side' comparison fastatail Drop the first 'n' bases fastatranslate Convert DNA sequences to one-letter protein sequences amplify Predict PCR product from primers and template The 'amplify' program for generating predicted PCR products is useful for designing primers and cloning strategies and is an example of how the core fasta* utilities can be combined using pipes for more complex tasks. It depends on the 'kalign' program, available at: http://www.ebi.ac.uk/Tools/msa/kalign/