Flexible protein database based on amino acid k-mers

Identification of proteins is one of the most computationally intensive steps in genomics studies. It usually relies on aligners that do not accommodate rich information on proteins and require additional pipelining steps for protein identification. We introduce kAAmer, a protein database engine bas...

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Autores principales: Déraspe, Maxime, Boisvert, Sébastien, Laviolette, François, Roy, Paul H, Corbeil, Jacques
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2022
Materias:
Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9160020/
https://www.ncbi.nlm.nih.gov/pubmed/35650262
http://dx.doi.org/10.1038/s41598-022-12843-9
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author Déraspe, Maxime
Boisvert, Sébastien
Laviolette, François
Roy, Paul H
Corbeil, Jacques
author_facet Déraspe, Maxime
Boisvert, Sébastien
Laviolette, François
Roy, Paul H
Corbeil, Jacques
author_sort Déraspe, Maxime
collection PubMed
description Identification of proteins is one of the most computationally intensive steps in genomics studies. It usually relies on aligners that do not accommodate rich information on proteins and require additional pipelining steps for protein identification. We introduce kAAmer, a protein database engine based on amino-acid k-mers that provides efficient identification of proteins while supporting the incorporation of flexible annotations on these proteins. Moreover, the database is built to be used as a microservice, to be hosted and queried remotely.
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spelling pubmed-91600202022-06-03 Flexible protein database based on amino acid k-mers Déraspe, Maxime Boisvert, Sébastien Laviolette, François Roy, Paul H Corbeil, Jacques Sci Rep Article Identification of proteins is one of the most computationally intensive steps in genomics studies. It usually relies on aligners that do not accommodate rich information on proteins and require additional pipelining steps for protein identification. We introduce kAAmer, a protein database engine based on amino-acid k-mers that provides efficient identification of proteins while supporting the incorporation of flexible annotations on these proteins. Moreover, the database is built to be used as a microservice, to be hosted and queried remotely. Nature Publishing Group UK 2022-06-01 /pmc/articles/PMC9160020/ /pubmed/35650262 http://dx.doi.org/10.1038/s41598-022-12843-9 Text en © The Author(s) 2022 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Article
Déraspe, Maxime
Boisvert, Sébastien
Laviolette, François
Roy, Paul H
Corbeil, Jacques
Flexible protein database based on amino acid k-mers
title Flexible protein database based on amino acid k-mers
title_full Flexible protein database based on amino acid k-mers
title_fullStr Flexible protein database based on amino acid k-mers
title_full_unstemmed Flexible protein database based on amino acid k-mers
title_short Flexible protein database based on amino acid k-mers
title_sort flexible protein database based on amino acid k-mers
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9160020/
https://www.ncbi.nlm.nih.gov/pubmed/35650262
http://dx.doi.org/10.1038/s41598-022-12843-9
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