Tag: XML

XML2RAF 1.02 -Create RAF Maps from PDB XML files

XML2RAF 1.02

:: DESCRIPTION

XML2RAF is a Perl software to create RAF maps from PDB XML files.The Protein Data Bank provides XML files that include a mapping between the PDB-format records SEQRES (representing the sequence of the molecule used in an experiment) and ATOM (representing the atoms experimentally observed). These XML files (along with the PDB’s chemical dictionary) also provide information on the original identity of most residues prior to any post-translational modifications, including cyclizations.

::DEVELOPER

Computational Genomics Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 XML2RAF

:: MORE INFORMATION

Citation:

Chandonia JM, Hon G, Walker NS, Lo Conte L, Koehl P, Levitt M, Brenner SE.
The ASTRAL compendium in 2004.
Nucleic Acids Research 32:D189-D192 (2004).

PyMsXML 0.5.4 – Convert Vendor Specific Mass Spectrometry file formats to open XML file formats

PyMsXML 0.5.4

:: DESCRIPTION

PyMsXML is a python script for converting vendor specific mass spectrometry data files for Applied Biosystems’ Q-Star, 4700, 4800, Mariner, and Voyager mass spectrometers from their raw binary form, to either of the emerging XML file formats for mass spectra: mzXML, from the Sashimi Glossolalia project of the Institute for Systems Biology (ISB); and mzData, from the Proteome Standardization Initiative (PSI) project of the Human Proteome Organization (HUPO).

::DEVELOPER

Edwards Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Python

:: DOWNLOAD

 PyMsXML

:: MORE INFORMATION

KEGGscape 0.9.1 – File Reader and Pathway Vsualizer for KEGG XML (KGML) files

KEGGscape 0.9.1

:: DESCRIPTION

KEGGscape is a pathway data integration and visualization app for Cytoscape.

::DEVELOPER

KEGGscape team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux/ MacOsX
  • Cytoscape

:: DOWNLOAD

KEGGscape

:: MORE INFORMATION

Citation

KEGGscape: a Cytoscape app for pathway data integration.
Nishida K, Ono K, Kanaya S, Takahashi K.
F1000Res. 2014 Jul 1;3:144. doi: 10.12688/f1000research.4524.1

PRIDE Converter 2.5.7 – Converts Mass Spectrometry Data into PRIDE XML

PRIDE Converter 2.5.7

:: DESCRIPTION

PRIDE Converter 2 converts mass spectrometry data from most common data formats into valid PRIDE XML for submission to the publicly available PRIDE database. It presents a convenient, wizard-like graphical user interface, and includes efficient access to the Ontology Lookup Service.

::DEVELOPER

PRIDE Converter Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOSX
  • Java

:: DOWNLOAD

PRIDE Converter

:: MORE INFORMATION

Citation

Barsnes et. al:
PRIDE Converter: making proteomics data-sharing easy
Nat Biotechnol. 2009 Jul;27(7):598-9.

Cote RG & Griss J, et al.,
The PRIDE Converter 2 framework: an improved suite of tools to facilitate data submission to the PRIDE database and the ProteomeXchange consortium.
Mol Cell Proteomics. 2012 Sep 4.

OrthoXML 0.3 / SeqXML 0.4 – XML standards for Orthology and Sequence Information

OrthoXML 0.3 / SeqXML 0.4

:: DESCRIPTION

OrthoXML is designed broadly to allow the storage and comparison of orthology data from any ortholog database. It establishes a structure for describing orthology relationships while still allowing flexibility for database-specific information to be encapsulated in the same format.

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.

:: DEVELOPER

Sonnhammer Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

OrthoXML  / SeqXML

:: MORE INFORMATION

sff_extract 0.3.0 – Extract the reads from the sff files into Fasta / xml/ caf file

sff_extract 0.3.0

:: DESCRIPTION

sff_extract extracts the reads from the sff files and stores them into fasta and xml or caf text files. 454 sequence reads are usually stored in sff files. In these files the information about the reads is stored: sequence, quality and quality and adapter clips.

::DEVELOPER

Jose Blanca and Bastien Chevreux @ Bioinformatics at COMAV 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Python

:: DOWNLOAD

 sff_extract

:: MORE INFORMATION