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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.
Methods and Results
PepID – Rapid identification
of peptide sequences based on amino acid composition
The function of the PepID tool is to demonstrate the implementation of the
algorithm developed for the identification of peptides based on their composition
that has been developed as part of the MCW NHLBI Proteomics Center project.
This algorithm uses clustering techniques derived from data mining to generate
a hierarchical index of peptide amino acid attribute (PAA) vectors. A query
peptide composition derived from sequence or MS data is used as to identify
the matching peptide in the database using an indexed lookup. This method
is much less computationally intensive and therefore potentially faster than
the pair-wise methods of peptide identification currently used.
ProMoST – High precision mass and pK calculations
for native and modified proteins
Biologically, protein modifications are one of the most important regulators
protein function. It has been long known that many protein modifications lead
to a change in mass, and more importantly, a change in the charge of the protein.
These changes can be readily observed using 2 dimensional gel electrophoresis.
ProMoST allows for the calculation of high precision values for the molecular
mass and predicted pI for unmodified proteins and proteins with predefined
or user defined modifications. ProMoST allows the user to alter the pK values
used for the pI calculation and new modifications can be defined. The results
can be output as a text file or an Excel .xls file and/or visualized as a
table of calculated values or a graphic representation of a theoretical 2D
gel.
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