Vector sequence contamination of the Plasmodium vivax sequence database in PlasmoDB and In silico correction of 26 parasite sequences

We found a 47 aa protein sequence that occurs 17 times in the Plasmodium vivax nucleotide database published on PlasmoDB. Coding sequence analysis showed multiple restriction enzyme sites within the 141 bp nucleotide sequence, and a His6 tag attached to the 3’ end, suggesting cloning vector origins....

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Autores principales: Tao, Zhi-Yong, Sui, Xu, Jun, Cao, Culleton, Richard, Fang, Qiang, Xia, Hui, Gao, Qi
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2015
Materias:
Letter to the Editor
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4464627/
https://www.ncbi.nlm.nih.gov/pubmed/26062606
http://dx.doi.org/10.1186/s13071-015-0927-x
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author Tao, Zhi-Yong
Sui, Xu
Jun, Cao
Culleton, Richard
Fang, Qiang
Xia, Hui
Gao, Qi
author_facet Tao, Zhi-Yong
Sui, Xu
Jun, Cao
Culleton, Richard
Fang, Qiang
Xia, Hui
Gao, Qi
author_sort Tao, Zhi-Yong
collection PubMed
description We found a 47 aa protein sequence that occurs 17 times in the Plasmodium vivax nucleotide database published on PlasmoDB. Coding sequence analysis showed multiple restriction enzyme sites within the 141 bp nucleotide sequence, and a His6 tag attached to the 3’ end, suggesting cloning vector origins. Sequences with vector contamination were submitted to NCBI, and BLASTN was used to cross-examine whole-genome shotgun contigs (WGS) from four recently deposited P. vivax whole genome sequencing projects. There are at least 26 genes listed in the PlasmoDB database that incorporate this cloning vector sequence into their predicted provisional protein products.
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spelling pubmed-44646272015-06-14 Vector sequence contamination of the Plasmodium vivax sequence database in PlasmoDB and In silico correction of 26 parasite sequences Tao, Zhi-Yong Sui, Xu Jun, Cao Culleton, Richard Fang, Qiang Xia, Hui Gao, Qi Parasit Vectors Letter to the Editor We found a 47 aa protein sequence that occurs 17 times in the Plasmodium vivax nucleotide database published on PlasmoDB. Coding sequence analysis showed multiple restriction enzyme sites within the 141 bp nucleotide sequence, and a His6 tag attached to the 3’ end, suggesting cloning vector origins. Sequences with vector contamination were submitted to NCBI, and BLASTN was used to cross-examine whole-genome shotgun contigs (WGS) from four recently deposited P. vivax whole genome sequencing projects. There are at least 26 genes listed in the PlasmoDB database that incorporate this cloning vector sequence into their predicted provisional protein products. BioMed Central 2015-06-12 /pmc/articles/PMC4464627/ /pubmed/26062606 http://dx.doi.org/10.1186/s13071-015-0927-x Text en © Tao et al. 2015 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Letter to the Editor
Tao, Zhi-Yong
Sui, Xu
Jun, Cao
Culleton, Richard
Fang, Qiang
Xia, Hui
Gao, Qi
Vector sequence contamination of the Plasmodium vivax sequence database in PlasmoDB and In silico correction of 26 parasite sequences
title Vector sequence contamination of the Plasmodium vivax sequence database in PlasmoDB and In silico correction of 26 parasite sequences
title_full Vector sequence contamination of the Plasmodium vivax sequence database in PlasmoDB and In silico correction of 26 parasite sequences
title_fullStr Vector sequence contamination of the Plasmodium vivax sequence database in PlasmoDB and In silico correction of 26 parasite sequences
title_full_unstemmed Vector sequence contamination of the Plasmodium vivax sequence database in PlasmoDB and In silico correction of 26 parasite sequences
title_short Vector sequence contamination of the Plasmodium vivax sequence database in PlasmoDB and In silico correction of 26 parasite sequences
title_sort vector sequence contamination of the plasmodium vivax sequence database in plasmodb and in silico correction of 26 parasite sequences
topic Letter to the Editor
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4464627/
https://www.ncbi.nlm.nih.gov/pubmed/26062606
http://dx.doi.org/10.1186/s13071-015-0927-x
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