This tool is designed to accept a GenBank or EMBL format file, and convert it to a FASTA file. You have control over what kind of sequence gets extracted, and how the header line is written. Select a GenBank or EMBL format file to upload containing a feature table. Select the file format. Choose the delimiter characters that will separate the qualifiers from one another in the header line. Select whether to extract translated amino acid sequences, DNA sequence for each feature, or the entire DNA sequence of the whole record. To choose how your header line appears, designate the names of the qualifiers, one per field, in the order that you want them to appear in the FASTA header line. Common feature and qualifier choices are already filled in, but you may put your own choices in their place. A description of potential feature keys and qualifiers can be found here.
A stand alone command line version of this software is available here.Please only process one file at a time, so as not to overload our server. If your input file is more than a few MB, please download the stand alone version.
Support for the development of Convert GenBank to FASTA provided by the National Science Foundation under Grant EF-0523756 to G. Rocap and R. A. Cattolico.
Any opinions, findings and conclusions or recomendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation (NSF)
Genbank to FASTAby Cedar McKay and Gabrielle Rocap, UW Oceanography is licensed under a Creative Commons Attribution-ShareAlike 3.0 Unported License.