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

BMC Bioinformatics

Software

Krupa Arun Navalkar¹  Jack S Emery¹  Rebecca F Halperin¹  Stephen Albert Johnston¹  Phillip Stafford¹ 

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

关键词: Phage Display;    Epitope Prediction;    Amino Acid Frequency;    Peptide Array;    Antibody Epitope;   

DOI  :  10.1186/1471-2105-13-1

 received in 2011-09-19, accepted in 2012-01-03,  发布年份 2012

来源: Springer

【 摘 要 】

BackgroundRandom-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.ResultsGuiTope 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.ConclusionsGuiTope 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 and ongoing updates and source code will be available at sourceforge.net.

【 授权许可】

Unknown   
© Halperin et al; licensee BioMed Central Ltd. 2012. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.