Sequence files

The HMM software can automatically recognize and parse a number of common file formats. These formats are listed below. If you know your sequence database is in one of these formats, you can use the file. If you are typing sequences in manually and want to know how to format them, see the section of FASTA format below for unaligned sequences, and the section on SELEX format for alignments.

• Single sequence formats
• Multiple unaligned sequences (databases)
• Alignments
• Warnings
• FASTA unaligned sequence format
  • Example of a simple FASTA file
• SELEX alignment format
  • Example of a simple SELEX format file
  • Detailed specification of a SELEX file
  • Optional annotation
  • Secondary structure
  • Reference coordinate system
  • Sequence header
  • Author
  • An example SELEX file with annotation