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About PepArray pro

 PepArray pro is a proteomics tool to provide PepArray Layout file that contains information about peptides, peptide IDs, and the array-location of the peptides to be synthesized on chip.  The Layout file is required by the synthesis of an addressable peptide microarray.  Peptide microarrays (PepArrays) provide powerful proteomics technology platform for a broad range of applications in studying the interactions between protein-protein, protein-nucleic acid, and many other intermolecular interactions as signatures to cellular signaling pathways, and regulatory network activities.  Such studies can be applied to not only basic research but also clinical biomedical tool development such as biomarker detection, diagnostic reagent discovery, drug development, and many more.

PepArray pro supports the generation of peptide sequences containing standard or non-standard amino acids from reading user-input sequences, importing from web resources, or modifying existing peptides.  Currently, phosphopeptides from the corresponding databases Phospho.ELM and PepCyber P~PEP are also supported. The designed Layout file can incorporate reference and/or control peptides for quality of synthesis and assay, generate peptide modifications, replicate the generated peptides, and provide design statistics.  The designed PepArrays can be stored and archived.  PepArray pro makes available of a set of catalog PepArray Layout files.

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Design PepArray

Enter parameters for rows and columns for an array

I.  Define peptides of a panel
    a. Select SEED peptides
    b. Derive peptides related to SEEDs
    c. Write controls (peptides, blank, etc.)
    d. Define number of replicates
    e. Make final peptide selections
II.  Repeat I for a second panel of peptides
III.  Select the panels to be included in       PepArray
IV.  Save the Layout file(optional)

Write the design array into an output file (containing specific row and column address for each peptide)

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