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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/
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