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 language | English |
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Title of host publication | Research in Computational Molecular Biology - 22nd Annual International Conference, RECOMB 2018, Proceedings |
Editors | Benjamin J. Raphael |
Publisher | Springer Verlag |
Pages | 154-166 |
Number of pages | 13 |
ISBN (Print) | 9783319899282 |
DOIs | |
State | Published - 2018 |
Externally published | Yes |
Event | 22nd International Conference on Research in Computational Molecular Biology, RECOMB 2018 - Paris, France Duration: 21 Apr 2018 → 24 Apr 2018 |
Publication series
Name | Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) |
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Volume | 10812 LNBI |
ISSN (Print) | 0302-9743 |
ISSN (Electronic) | 1611-3349 |
Conference
Conference | 22nd International Conference on Research in Computational Molecular Biology, RECOMB 2018 |
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Country/Territory | France |
City | Paris |
Period | 21/04/18 → 24/04/18 |
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