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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.
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BMC Bioinformatics

ISSN: 1471-2105

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