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Table 2 Comparison of native formats and their HOBIT XML counterparts

From: XML schemas for common bioinformatic data types and their application in workflow systems

Sequence formats   
FASTA SequenceML simple sequence information for nucleic and amino acids
GCG SequenceAnnotationML sequence information with additional facilities for annotations
STADEN   
Sequence alignment formats
FASTA AlignmentML (multiple) alignments for nucleic and amino acids
CLUSTAL   
MSF   
RNA secondary structure formats
mFOLD RNAStructML RNA secondary structure information
Vienna style DotBracket   
RNA Secondary Structure Alignment Formats
aligned Vienna style DotBracket RNAStructAlignmentML (multiple) alignments of RNA secondary structures
  1. The table shows a comparison of some native bioinformatic file formats (first column) and their HOBIT XML counterparts (second column). These XML formats cover sequence, alignment, RNA secondary structure and RNA secondary structure alignment formats in a form that is independent of any specific program. The usage of the XML formats leads to a significant decrease in the number of necessary file formats.