Convert MSF alignment to UCSC nib

Provided by bugaco.com

Convert a MSF alignment sequence file to UCSC nib.

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

MSF alignment → UCSC nib

  • This output format holds exactly one sequence. Upload a file with a single record.
  • UCSC nib stores only the DNA letters A, C, G, T, and N. Gaps, ambiguity codes, RNA (U), and protein letters are rejected.
  • UCSC nib does not store record names, so the output has no identifier.
  • 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.

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.msf", "msf",
                      "output.nib", "nib")
print("Converted %i records" % count)

Sample input file: MSF alignment

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

Download sample (sample.msf, 2.3 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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