Reverse de Bruijn: Utilizing Reverse Peptide Synthesis to Cover All Amino Acid k-mers

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

Abstract

Peptide arrays measure the binding intensity of a specific protein to thousands of amino acid peptides. By using peptides that cover all k-mers, a comprehensive picture of the binding spectrum is obtained. Researchers would like to measure binding to the longest k-mer possible, but are constrained by the number of peptides that can fit into a single microarray. A key challenge is designing a minimum number of peptides that cover all k-mers. Here, we suggest a novel idea to reduce the length of the sequence covering all k-mers by utilizing a unique property of the peptide synthesis process. Since the synthesis can start from both ends of the peptide template, it is enough to cover each k-mer or its reverse, and use the same template twice: in forward and reverse. Then, the computational problem is to generate a minimum length sequence that for each k-mer either contains it or its reverse. We developed an algorithm ReverseCAKE to generate such a sequence. ReverseCAKE runs in time linear in the output size and is guaranteed to produce a sequence that is longer by at most Θ(nlogn) characters compared to the optimum n. The obtained saving factor by ReverseCAKE approaches the theoretical lower bound as k increases. In addition, we formulated the problem as an integer linear program and empirically observed that the solutions obtained by ReverseCAKE are near-optimal. Through this work we enable more effective design of peptide microarrays.

Original languageEnglish
Title of host publicationResearch in Computational Molecular Biology - 22nd Annual International Conference, RECOMB 2018, Proceedings
EditorsBenjamin J. Raphael
PublisherSpringer Verlag
Pages154-166
Number of pages13
ISBN (Print)9783319899282
DOIs
StatePublished - 2018
Externally publishedYes
Event22nd International Conference on Research in Computational Molecular Biology, RECOMB 2018 - Paris, France
Duration: 21 Apr 201824 Apr 2018

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume10812 LNBI
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Conference

Conference22nd International Conference on Research in Computational Molecular Biology, RECOMB 2018
Country/TerritoryFrance
CityParis
Period21/04/1824/04/18

Bibliographical note

Publisher Copyright:
© Springer International Publishing AG, part of Springer Nature 2018.

Keywords

  • Array design
  • Peptide array
  • Reverse synthesis
  • de Bruijn graph
  • de Bruijn sequence

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