ProteomeCommons.org JAF: reference information and tools for proteomics

Analysis of proteomics data, specifically mass spectrometry data, commonly relies on libraries of known information such as atomic masses, known stable isotopes, atomic compositions of amino acids, observed modifications of known amino acids and ion masses that directly correspond to known amino aci...

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Bibliographic Details
Published in:Bioinformatics 2006-03, Vol.22 (5), p.632-633
Main Authors: Falkner, J. A., Falkner, J. W., Andrews, P. C.
Format: Article
Language:English
Subjects:
Biological and medical sciences
Database Management Systems
Databases, Protein
Documentation - methods
Fundamental and applied biological sciences. Psychology
General aspects
Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects)
Peptide Mapping - methods
Proteins - analysis
Proteins - chemistry
Proteins - classification
Proteomics - methods
Sequence Analysis, Protein - methods
Software
User-Computer Interface
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Description
Summary:Analysis of proteomics data, specifically mass spectrometry data, commonly relies on libraries of known information such as atomic masses, known stable isotopes, atomic compositions of amino acids, observed modifications of known amino acids and ion masses that directly correspond to known amino acid sequences. The Java Analysis Framework (JAF) for proteomics provides a freely usable, open-source library of Java code that abstracts all of the aforementioned data, enabling more rapid development of proteomics tools. The JAF also includes several user tools that can be run directly from a web browser. Availability: The current version and an archive of all older versions of the Java Analysis Framework for Proteomics is freely available, including complete source-code, at Contact:jfalkner@umich.edu
ISSN:1367-4803
1460-2059
1367-4811
DOI:10.1093/bioinformatics/btk015