Convert Stockholm alignment to IMGT (EMBL variant)

Provided by bugaco.com

Convert a Stockholm alignment sequence file to IMGT (EMBL variant).

This output needs a sequence type. The selected input format does not record it, so the converter will use your choice.

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

Stockholm alignment → IMGT (EMBL variant)

  • Only the aligned sequence rows are converted; alignment annotations such as scores and consensus lines are not kept. A file with several alignments can be converted only to sequence formats such as FASTA.
  • The output writes every sequence letter in the same case, so lowercase (soft-masked) regions are no longer marked.

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 output needs a sequence type, so replace the example molecule type with DNA, RNA, or protein to match your file.

from Bio import SeqIO

count = SeqIO.convert("input.stockholm", "stockholm",
                      "output.imgt", "imgt",
                      molecule_type="DNA")
print("Converted %i records" % count)

Sample input file: Stockholm alignment

Copy this example into a file, or download it, to try a Stockholm alignment conversion.

Download sample (sample.sto, 299 bytes)

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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