This is a short description of the biodom WebService at BiBiServ.
If you're not familiar with using webservices in general you should have a closer look to our webservice related linklist.

biodomws consists of four services (AlignmentML, SequenceML, RNAStructML and RNAStructAlignmentML) for converting native formats in xml and back. Each service has its own functions, which are desribed below. Contrary to most of the other Webservices at BiBiServ, all functions of this service return directly the result of the query.

AlignmentML
AlignmentML is a XML schema with the grammar for representing multiple sequence alignments

function	input	output	description
fromFasta	FASTA as string Score as Integer SequenceType as int	AlignmentML as XML	converting FASTA to an AlignmentML XML Document
fromClustal	clustal as string Score as Integer SequenceType as int	AlignmentML as XML	converting clustal to an AlignmentML XML Document
toFasta	AlignmentML as XML	FASTA as string	retrieving FASTA from an AlignmentML XML Document

SequenceML
SequenceML is a XML schema with the grammar for representing multiple sequences with some meta information (FASTA replacement)

function	input	output	description
fromFasta	FASTA as string SequenceType as int	SequenceML as XML	converting FASTA to an SequenceML XML Document
toFasta	SequenceML as XML	FASTA as string	retrieving FASTA from an SequenceML XML Document

RNAStructML
RNAStructML is a XML schema with the grammar for representing RNA secondary structure information

function	input	output	description
fromDotBracketFasta	DotBracketFasta as String	RNAStructML as XML	converting DotBracketFasta to an RNAStructML XML Document
toDotBracketFasta	RNAStructML as XML	DotBracketFasta as string	retrieving DotBracketFasta from an RNAStructML XML Document

RNAStructAlignmentML
RNAStructAlignmentML is a XML schema with the grammar for representing multiple RNA secondary structure alignments

function	input	output	description
fromAlignedDotBracketFasta	AlignedDotBracketFasta as String	RNAStructAlignmentML as XML	converting Aligned DotBracketFasta to an RNAStructAlignmentML XML Document
toAlignedDotBracketFasta	RNAStructAlignmentML as XML	AlignedDotBracketFasta as string	retrieving AlignedDotBracketFasta from an RNAStructAlignmentML XML Document

Sequence Type	Value
NucleicAcid	0
AminoAcid	1
Free Sequence	2
Empty Sequence	3
Unknown Sequence Type	4

The Example Java clients are based on Apache Axis.
biodomwsCAlignmentMLtoFasta.java, alignmentml.xml
biodomwsCSequenceMLtoFasta.java, sequenceml.xml
biodomwsCAlignmentMLfromFasta.java
biodomwsCAlignmentMLfromClustal.java
biodomwsCSequenceMLfromFasta.java

The example perl clients are based on SOAP::Lite.
biodomwsCSequenceMLfromFasta.pl, fasta.fas
biodomwsCAlignmentMLfromFasta.pl, fasta.fas
biodomwsCAlignmentMLfromClustal.pl, clustal.clu