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Database ◽  
2020 ◽  
Vol 2020 ◽  
Author(s):  
Alejandro Rubio ◽  
Pablo Mier ◽  
Miguel A Andrade-Navarro ◽  
Andrés Garzón ◽  
Juan Jiménez ◽  
...  

Abstract The genomics era is resulting in the generation of a plethora of biological sequences that are usually stored in public databases. There are many computational tools that facilitate the annotation of these sequences, but sometimes they produce mistakes that enter the databases and can be propagated when erroneous data are used for secondary analyses, such as gene prediction or homology searching. While developing a computational gene finder based on protein-coding sequences, we discovered that the reference UniProtKB protein database is contaminated with some spurious sequences translated from DNA containing clustered regularly interspaced short palindromic repeats. We therefore encourage developers of prokaryotic computational gene finders and protein database curators to consider this source of error.


2017 ◽  
Vol 63 (12) ◽  
pp. 970-983 ◽  
Author(s):  
Jordyn Bergsveinson ◽  
Barry Ziola

Beer-spoilage-related lactic acid bacteria (BSR LAB) belong to multiple genera and species; however, beer-spoilage capacity is isolate-specific and partially acquired via horizontal gene transfer within the brewing environment. Thus, the extent to which genus-, species-, or environment- (i.e., brewery-) level genetic variability influences beer-spoilage phenotype is unknown. Publicly available Lactobacillus brevis genomes were analyzed via BlAst Diagnostic Gene findEr (BADGE) for BSR genes and assessed for pangenomic relationships. Also analyzed were functional coding capacities of plasmids of LAB inhabiting extreme niche environments. Considerable genetic variation was observed in L. brevis isolated from clinical samples, whereas 16 candidate genes distinguish BSR and non-BSR L. brevis genomes. These genes are related to nutrient scavenging of gluconate or pentoses, mannose, and metabolism of pectin. BSR L. brevis isolates also have higher average nucleotide identity and stronger pangenome association with one another, though isolation source (i.e., specific brewery) also appears to influence the plasmid coding capacity of BSR LAB. Finally, it is shown that niche-specific adaptation and phenotype are plasmid-encoded for both BSR and non-BSR LAB. The ultimate combination of plasmid-encoded genes dictates the ability of L. brevis to survive in the most extreme beer environment, namely, gassed (i.e., pressurized) beer.


PLoS ONE ◽  
2016 ◽  
Vol 11 (3) ◽  
pp. e0152747 ◽  
Author(s):  
Jürgen Behr ◽  
Andreas J. Geissler ◽  
Jonas Schmid ◽  
Anja Zehe ◽  
Rudi F. Vogel

2011 ◽  
Vol 21 (9) ◽  
pp. 1529-1542 ◽  
Author(s):  
M. Yandell ◽  
C. Huff ◽  
H. Hu ◽  
M. Singleton ◽  
B. Moore ◽  
...  

PLoS ONE ◽  
2009 ◽  
Vol 4 (5) ◽  
pp. e5433 ◽  
Author(s):  
Raheleh Salari ◽  
Cagri Aksay ◽  
Emre Karakoc ◽  
Peter J. Unrau ◽  
Iman Hajirasouliha ◽  
...  
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