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 |