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Open Access Highly Accessed Software

GuiTope: an application for mapping random-sequence peptides to protein sequences

Rebecca F Halperin, Phillip Stafford, Jack S Emery, Krupa Arun Navalkar and Stephen Albert Johnston*

Author Affiliations

Center for Innovations in Medicine, The Biodesign Institute at Arizona State University, PO Box 875901, Tempe AZ 85281, USA

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BMC Bioinformatics 2012, 13:1  doi:10.1186/1471-2105-13-1

Published: 3 January 2012

Abstract

Background

Random-sequence peptide libraries are a commonly used tool to identify novel ligands for binding antibodies, other proteins, and small molecules. It is often of interest to compare the selected peptide sequences to the natural protein binding partners to infer the exact binding site or the importance of particular residues. The ability to search a set of sequences for similarity to a set of peptides may sometimes enable the prediction of an antibody epitope or a novel binding partner. We have developed a software application designed specifically for this task.

Results

GuiTope provides a graphical user interface for aligning peptide sequences to protein sequences. All alignment parameters are accessible to the user including the ability to specify the amino acid frequency in the peptide library; these frequencies often differ significantly from those assumed by popular alignment programs. It also includes a novel feature to align di-peptide inversions, which we have found improves the accuracy of antibody epitope prediction from peptide microarray data and shows utility in analyzing phage display datasets. Finally, GuiTope can randomly select peptides from a given library to estimate a null distribution of scores and calculate statistical significance.

Conclusions

GuiTope provides a convenient method for comparing selected peptide sequences to protein sequences, including flexible alignment parameters, novel alignment features, ability to search a database, and statistical significance of results. The software is available as an executable (for PC) at http://www.immunosignature.com/software webcite and ongoing updates and source code will be available at sourceforge.net.