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Component: Bioinformatics
Component Bioinformatics focuses on data warehousing, implementation of data
analysis and data mining tools, development of novel algorithms and databases
in support of proteomic studies.
Please choose the folowing items to find more information about this
component.
Highlights of activities for the current quarter (07-
09/2003)
Informatics infrastructure
- Public web site for the MCW-NHLBI Proteomics Center has been migrated to
a dedicated Sun 280 server.
- CVS system to manage software development has been installed, current proteomics
programming projects have been migrated to the CVS repository.
- Initial review of the existing database schemas for proteomics data has
been completed.
- In collaboration with the members of the Protein Analysis and Technology
Implementation component a preliminary schema for the CPDP database has been
designed to take advantage of the relevant components of the PGA and RGD databases.
Novel Proteomics Tools
- PepID
The peptide identification tool (PepID) has been further refined and extended
to allow for the identification of both individual peptides and whole proteins
in either single entry or batch modes.
A beta version of the PepID program with a
web interface is now available.
The software that generates the indexed databases required for peptide
identification has been translated from PERL to C++ and has been optimized
for increased speed. Additional databases containing data from rat, mouse,
human and other model organisms have been generated. Alpha versions of the
program required to determine amino acid composition from MS data have been
developed and are being tested with sample data provided by the Technology
Development component of the project and a standardized test MS data set
from the Institute for System Biology in Seattle.
- ProMoST
The Protein Modification Screening Tool (ProMoST) is a program to calculate
accurate MWT and pI values from proteins.
A beta version of the ProMoST program with
a web interface is now available.
Presentation and Publications
A talk describing the algorithm developed for identifying peptides from
amino acid composition data and the PepID program was presented as part of
the proteomics session of the Cold Spring Harbor Laboratory Genome Informatics
Meeting in May 2003. Publications describing the PepID indexing algorithm
and its applications are in preparation.
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