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OrthoXML & SeqXML

The SeqXML schema (XSD) defines the skeletal structure of the sequence files and allows one to set constraints for each type of data it contains: for example, one can limit a DNA sequence to consist only of {A,G,C,T,N}. If one then tries to import a DNA sequence containing a 'Z', this error will be detected automatically by any XML validator. For documentation, click here. For documentation, click here. Two common data management issues for orthology databases are:. To make these tasks easier, SeqXML.

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OrthoXML & SeqXML | orthoxml.org Reviews

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The SeqXML schema (XSD) defines the skeletal structure of the sequence files and allows one to set constraints for each type of data it contains: for example, one can limit a DNA sequence to consist only of {A,G,C,T,N}. If one then tries to import a DNA sequence containing a 'Z', this error will be detected automatically by any XML validator. For documentation, click here. For documentation, click here. Two common data management issues for orthology databases are:. To make these tasks easier, SeqXML.

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OrthoXML & SeqXML | orthoxml.org Reviews

https://orthoxml.org

The SeqXML schema (XSD) defines the skeletal structure of the sequence files and allows one to set constraints for each type of data it contains: for example, one can limit a DNA sequence to consist only of {A,G,C,T,N}. If one then tries to import a DNA sequence containing a 'Z', this error will be detected automatically by any XML validator. For documentation, click here. For documentation, click here. Two common data management issues for orthology databases are:. To make these tasks easier, SeqXML.

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orthoxml.org

1

BioJava

http://www.orthoxml.org/xml/BioJava.html

SeqXML BioJava support (Version 0.3 only! Biojava-seqxml-1.0.tar.gz. Reading with the standard BioJava IOTools:. ClassforName(org.biojavax.bio.seq.io.SeqXMLFormat);. Namespace ns = RichObjectFactory.getDefaultNamespace();. RichSequenceIterator seqs = RichSequence.IOTools.readFile(seqXMLFile,ns);. Import org.biojavax.bio.seq.io.SeqXMLFormat;. RichSequenceFormat seqXMLWrite = new SeqXMLFormat();. SeqXMLWrite.setPrintStream(System.out);. SeqXMLWrite.writeSequence(seqs.nextRichSequence() ,ns);.

2

Biopython Old

http://www.orthoxml.org/xml/Biopython_Old.html

Reading with the standard BioPython. From Bio import SeqIO. FileHandle = open(SEQXML FILE,r). Records = list(SeqIO.parse(fileHandle, seqxml). Writing with the standard BioPython. From Bio import SeqIO. SeqIOwrite(records,sys.stdout,seqxml).

3

Documentation

http://www.orthoxml.org/xml/Documentation.html

OrthoXML version 0.3. SeqXML version 0.4. Have questions or suggestions? OrthoXML example v0.3. SeqXML example v0.4.

4

Reference proteomes

http://www.orthoxml.org/xml/Reference_proteomes.html

SeqXML versions of the reference proteomes. Release 5 (2011 04). All 66 species in one tarball. FASTA versions available at. The Reference Proteomes group provides complete non-redundant proteome sets for species chosen by the Quest for Orthologs. Group 66 species are publicly available and are generated using UniProt and/or Ensembl. More information is available from our partners at the EBI. And at the Reference Genome Annotation Project. Have questions or suggestions?

5

OrthoXML Documentation

http://www.orthoxml.org/0.3/orthoxml_doc_v0.3.html

OrthoXML is an XML schema designed to describe orthology relations. Orthologs are defined as genes in different species deriving from a single gene in the last common ancestor. This relationship makes them interesting, as they are likely to have the same function. This document describes the content of OrthoXML version 0.2 and gives details about each element and attribute. In this section we describe the structure of an OrthoXML file. We will not go through the whole schema piece by piece but rather...

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OMA stand-alone

http://omabrowser.org/standalone

You can run OMA as a stand-alone program. Included are the algorithms for OMA itself plus its addition ESPRIT. The software can be installed on Linux (x86, both 64bit and 32bit) and MacOSX (x86, both 32bit and 64bit). For a short summary and pointers to detailed algorithmic publications of OMA, please refer to the OMA browser page:. For background info on ESPRIT, please refer to this article:. Http:/ dx.doi.org/10.1093/bib/bbr038. Infethz.ch or christophe.dessimoz at. After installation, make sure the.

questfororthologs.org

standards - Quest For Orthologs

http://questfororthologs.org/standards

Schmitt et al., Brief Bioinform 2011. Newick to OrthoXML converter, based on ETE. 160; Back to top. 160; Sitemap. 160; Log In. 160; Old revisions. Under the hood . Last modified: 2013/07/26 11:21 by.

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orthoxml.org

OrthoXML & SeqXML

The SeqXML schema (XSD) defines the skeletal structure of the sequence files and allows one to set constraints for each type of data it contains: for example, one can limit a DNA sequence to consist only of {A,G,C,T,N}. If one then tries to import a DNA sequence containing a 'Z', this error will be detected automatically by any XML validator. For documentation, click here. For documentation, click here. Two common data management issues for orthology databases are:. To make these tasks easier, SeqXML.

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