Base-Calling Algorithm with Vocabulary (BCV) Method for Analyzing Population Sequencing Chromatograms

Fantin, Yuri S.; Neverov, Alexey D.; Favorov, Alexander V.; Alvarez-Figueroa, Maria V.; Braslavskaya, Svetlana I.; Gordukova, Maria; Karandashova, I.V.; Kuleshov, Konstantin V.; Myznikova, Anna I.; Polishchuk, M. S.; Reshetov, Denis A.; Voiciehovskaya, Yana A.; Миронов, А.; Chulanov, Vladimir

doi:10.1371/journal.pone.0054835

Cited by 14 publications

(8 citation statements)

References 59 publications

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“…tyzzeri mixture by Ion Torrent. Although computational deciphering of mixed Sanger chromatograms is practiced, these situations are usually resolved by cloning amplicons: a time-consuming and expensive procedure (Carr et al, 2009;Fantin et al, 2013;Paparini et al, 2012. The results from this study, supports HTS as a better means for the identification of mixed infections.…”

Section: Discussionsupporting

confidence: 62%

Comparison of Sanger and next generation sequencing performance for genotyping Cryptosporidium isolates at the 18S rRNA and actin loci

Paparini

Gofton

Yang

et al. 2015

Experimental Parasitology

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This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. 47parvum isolates when deep sequenced but were undetected in Sanger sequencing. 48Sanger was cheaper than Ion Torrent when sequencing a small numbers of samples, 49 but when larger numbers of samples are considered (n=60), the costs were comparative. 50Fusion-tagged amplicon based approaches are a powerful way of approaching mixtures, the 51 only draw-back being the loss of PCR efficiency on low-template samples when using 52 primers coupled to MID tags and adaptors. Taken together these data show that HTS has 53 excellent potential for revealing the "true" composition of species/types in a Cryptosporidium 54 infection, but that HTS workflows need to be carefully developed to ensure sensitivity, 55 accuracy and contamination are controlled.

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Section: Discussionsupporting

confidence: 62%

Comparison of Sanger and next generation sequencing performance for genotyping Cryptosporidium isolates at the 18S rRNA and actin loci

Paparini

Gofton

Yang

et al. 2015

Experimental Parasitology

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“…The size of PCR products were detected by agarose gel electrophoresis. The amplified fragment was then sequenced and analyzed in the BLAST server (http://www.ncbi.nlm.nih.gov/BLAST; Greisen et al 1994;Fantin et al 2013).…”

Section: Molecular Identification Of the Selected Isolatementioning

confidence: 99%

Response surface methodology designation for optimization of lactic acid production by Streptococcus thermophilus isolated from industrial yogurt

Adibi¹,

Naghavi

Zohrabi³

2022

Nova Biotechnol. Chim.

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Using inexpensive sources is a crucial point in the production of valuable compounds such as lactic acid. In the present study, the production of lactic acid by an efficient isolate of S. thermophilus was optimized using whey as a carbon source and yeast extract as a nitrogen source. MRS culture medium with 6.5 % NaCl was used for the isolation of streptococci from industrial yogurt samples and the selected isolate was identified using the 16S rRNA gene sequencing. Evaluation of lactic acid production was done by the Randox method. Lactic acid production by the selected isolate was optimized by response surface methodology (RSM) in MRS broth regarding to different concentrations of whey and yeast extract. The isolate that produced the highest amount (8.9 g.L-1) of lactic acid within 52 h growth in MRS broth was identified as a strain of S. thermophilus by molecular identification. Optimization of concentrations of carbon and nitrogen sources resulted in the induction of lactic acid production by Streptococcus thermophilus up to 24.18 g.L-1 in the presence of 3.5 % of whey and 5 % of yeast extract as external carbon and nitrogen sources in the MRS medium, which was similar to the value predicted by RSM. Yeast extract was found to be more effective on lactic acid production than whey. Optimization of lactic acid production by low-cost substrates whey and yeast extract resulted in high induction of lactic acid production by S. thermophilus compared to some other studies that used other cost-effective substrates and/or bacteria isolated from traditional dairy products.

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“…Finally, we build long contigs by traversing the overlap graph built on short contigs, where selected references are used as constraints on possible paths, providing information about long-range linkage of short contigs. A similar idea was previously used for analysis of mixed chromatograms for the direct Sanger sequencing method [34]. The graph traversing algorithm links the unvisited short contigs, which have common references in their reference sets into haplotypes, and then penalizes already visited contigs at the subsequent iterations.…”

Section: Reference Selectionmentioning

confidence: 99%

VirGenA: a reference-based assembler for variable viral genomes

Fedonin

Fantin

Favorov

et al. 2017

Briefings in Bioinformatics

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Characterization of the within-host genetic diversity of viral pathogens is required for selection of effective treatment of some important viral infections, e.g. HIV, HBV and HCV. Despite the technical ability of detection, there are conflicting data regarding the clinical significance of low-frequency variants, partially because of the difficulty of their distinguishing from experimental artifacts. The issue of cross-contamination is relevant for all highly sensitive techniques, including deep sequencing: even trace contamination leads to a significant increase of false positives in identified SNVs. Determination of infections by multiple genotypes of some viruses, the incidence of which can be considerable, especially in risk groups, is also clinically significant in some cases. We developed a new viral reference-guided assembler, VirGenA, that can separate mixtures of strains of different intraspecies genetic groups (genotypes, subtypes, clades, etc.) and assemble a separate consensus sequence for each group in a mixture. It produced long assemblies for mixture components of extremely low frequencies (<1%) allowing detection of cross-contamination of samples by divergent genotypes. We tested VirGenA on both clinical and simulated data. On both types of data, VirGenA shows better or similar results than the existing de novo assemblers. Cross-platform implementation (including source code) is freely available at https://github.com/gFedonin/VirGenA/releases.

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Base-Calling Algorithm with Vocabulary (BCV) Method for Analyzing Population Sequencing Chromatograms

Cited by 14 publications

References 59 publications

Comparison of Sanger and next generation sequencing performance for genotyping Cryptosporidium isolates at the 18S rRNA and actin loci

Comparison of Sanger and next generation sequencing performance for genotyping Cryptosporidium isolates at the 18S rRNA and actin loci

Response surface methodology designation for optimization of lactic acid production by Streptococcus thermophilus isolated from industrial yogurt

VirGenA: a reference-based assembler for variable viral genomes

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