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Convert Genbank to Fasta

This page is designed to accept a genbank format file, and convert to a fasta file. You have control over what kind of sequence gets extracted, and how the title line is written


Instructions:

Select a genbank format file containing a feature table. Select whether to extract translated peptide sequences, DNA sequence for each feature, or the entire DNA sequence of the whole record. If you chose "Peptide Sequence", your feature table must have "translation" sub-features. To choose how your title line appears, designate the names of the sub-features, one per field, in the order that you want them to appear in the fasta title line. Common feature choices are already filled in, but you may put your own arbitrary features in their place. If you choose "DNA of Entire Record" you can't choose how your title line looks. Feature location is automatically included in title line. The given coordinates are for the whole feature, including introns.
Reasonable defaults are already entered, but feel free to make changes.
When you are ready, click "Make Fasta File!"


Please select a file to convert. Must be genbank format and have a feature table.


Output Sequence Type:
Peptide Sequence
Extracts peptide sequences from the feature table. Only works if your features include "translation" subfeatures.

Peptide sequence translated on the fly
Generates a translation from the nucleotide sequence on the fly. Useful if your genbank file doen't have "translation" subfeatures in the feature table. Does not take into account RNA editing. Also, where fuzzy locations are given, we just pick a spot. In some cases DNA sequences used in the translation will not be quite like actual cDNA that generated your protein, but should be close. For this reason, the above option that takes peptide sequence directly from the feature table is preferable.

DNA of each Feature
Takes into account joins, in other words, we are smart enough exclude introns in exported sequences. Does not take into account RNA editing. Also, where fuzzy locations are given, we just pick a spot. In some cases DNA sequence will not be quite like cDNA that generated your protein, but should be close.

DNA of entire record, not individual features.
If you select this option, you obviously can't select which features and subfeatures to extract. Those inputs will be ignored.


Feature to Extract:
CDS
rRNA
tRNA
gene
misc_RNA

Select subfeatures to use in the Title Line:
First Title:
Second Title:
Third Title:
Fourth Title:
Fifth Title:


Feature Position Information: Yes No
Insert into the title line at position:

Delimiter Character:
Space Pipe Space |
Tab
Space
Pipe |
Dash -
Underscore _

Ready?
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