Reverse de Bruijn: Utilizing Reverse Peptide Synthesis to Cover All Amino Acid k-mers.
Identifieur interne : 000096 ( Main/Merge ); précédent : 000095; suivant : 000097Reverse de Bruijn: Utilizing Reverse Peptide Synthesis to Cover All Amino Acid k-mers.
Auteurs : Yaron Orenstein [Israël]Source :
- Journal of computational biology : a journal of computational molecular cell biology [ 1557-8666 ] ; 2020.
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 to 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 the k-mer or its reverse. In this study, we present a new algorithm, called 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 mostΘ ( n log n ) characters compared with 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.
DOI: 10.1089/cmb.2019.0448
PubMed: 31995404
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<front><div type="abstract" xml:lang="en"><b>Peptide arrays measure the binding intensity of a specific protein to thousands of amino acid peptides. By using peptides that cover all <i>k</i>
-mers, a comprehensive picture of the binding spectrum is obtained. Researchers would like to measure binding to the longest <i>k</i>
-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 <i>k</i>
-mers. Here, we suggest a novel idea to reduce the length of the sequence covering all <i>k</i>
-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 <i>k</i>
-mer or its reverse and to use the same template twice: in forward and reverse. Then, the computational problem is to generate a minimum length sequence that for each <i>k</i>
-mer either contains the <i>k</i>
-mer or its reverse. In this study, we present a new algorithm, called 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</b>
<mml:math><mml:mi>Θ</mml:mi>
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<mml:mrow><mml:msqrt><mml:mrow><mml:mi>n</mml:mi>
</mml:mrow>
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<mml:mo>log</mml:mo>
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<b>characters compared with the optimum <i>n</i>
. The obtained saving factor by ReverseCAKE approaches the theoretical lower bound as <i>k</i>
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.</b>
</div>
</front>
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