Convert GenBank coding sequences (CDS) to Tab-separated (ID and sequence)

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Convert a GenBank coding sequences (CDS) sequence file to Tab-separated (ID and sequence).

Maximum file size: 50 MB. The file is checked before conversion.

GenBank coding sequences (CDS) → Tab-separated (ID and sequence)

  • Each CDS feature becomes one protein record built from its stated translation; the rest of the source record is not converted.
  • The output keeps only each record's ID, so description text (such as the words after the ID on a FASTA header line) is not kept.

About this conversion

The converter reads records in the input format and writes them in the output format. Data that the output format cannot store may be lost. The notes under the Convert file button list the important limits for this pair.

Run it with Biopython

For batch work, you can use Biopython's SeqIO.convert function. This pair needs no molecule type argument.

from Bio import SeqIO

count = SeqIO.convert("input.genbank-cds", "genbank-cds",
                      "output.tab", "tab")
print("Converted %i records" % count)

Sample input file: GenBank coding sequences (CDS)

Copy this example into a file, or download it, to try a GenBank coding sequences (CDS) conversion.

Download sample (sample.gb, 4.2 KB)

Samples are small illustrative files. Some come from the Biopython test suite (see the project's sample notes); they are not real study data.

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