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Export allele sequences in XMFA/concatenated FASTA formats - Helicobacter PubMLST

This script will export allele sequences in Extended Multi-FASTA (XMFA) format suitable for loading into third-party applications, such as ClonalFrame. It will also produce concatenated FASTA files. Only DNA loci that have a corresponding database containing allele sequence identifiers, or DNA and peptide loci with genome sequences tagged, can be included. Please check the loci that you would like to include. Alternatively select one or more schemes to include all loci that are members of the scheme. If a sequence does not exist in the remote database, it will be replaced with gap characters.

Aligned output is limited to 200 records; total output (records x loci) is limited to 1,000,000 sequences.

Please be aware that if you select the alignment option it may take a long time to generate the output file.

Select ids

Paste in list of ids to include, start a new
line for each. Leave blank to include all ids.

Include in identifier

If both allele designations and tagged sequences
exist for a locus, choose how you want these handled:

  • Include bp flanking sequence
  • Aligner: