Table 2.
Comparison of native formats and their HOBIT XML counterparts
| 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 |
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.