fasta-utils Files

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/