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Table 3 Available webservices supporting HOBIT XML formats

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

Name Description Supported formats (input/output)
CLUSTALW [18] general purpose multiple sequence alignment program SequenceML/AlignmentML
DCA [37] divide-and-conquer multiple sequence alignment program SequenceML/AlignmentML
Dialign [38] computation of an alignment based on segment-to-segment comparison SequenceML/AlignmentML
E2G [52] aligning genomic sequence to cDNA and EST data sets SequenceML/EBIApplicationResult
ITS2 [58-60] database of more than 20,000 rRNA internal transcribed spacer 2 (ITS2) secondary structures revealed by homology modeling -/RNAStructML
pknotsRG [61] RNA secondary structures folding, including the class of simple recursive pseudoknots SequenceML/RNAStructML
realsplice information about regulated alternative spliced genes -/SequenceAnnotationML
REPuter [62] computes all maximal duplications and reverse, complemented and reverse complemented repeats in a nucleic acid sequence SequenceML/EBIApplicationResult
RNAshapes [39] computation of a small set of representative structures of different shapes, computation of shape probabilities, and comparative prediction of consensus structures SequenceML/RNAStructML
RNAfold [19] RNA secondary structures folding SequenceML/RNAStructML