The WM-q multiple exact string matching algorithm for DNA sequences

The WM-q multiple exact string matching algorithm for DNA sequences

The string matching algorithms are among the essential fields in computer science, such as text search, intrusion detection systems, fraud detection, sequence search in bioinformatics. The exact string matching algorithms are divided into two parts: single and multiple. Multiple string matching algorithms involve finding elements of the pattern set P in a given input text T. String matching processes should be done in a time-efficient manner for DNA sequences. As the volume of the text T increases and the number of search patterns increases, the total runtime increases. Efficient algorithms should be selected to perform these search operations as soon as possible. In this study, the Wu-Manber algorithm, one of the multiple exact string matching algorithms, is improved.

Although the Wu-Manber algorithm is effective, it has some limitations, such as hash collisions. In this study, the WM-q algorithm, a version of the Wu-Manber algorithm based on the perfect hash function for DNA sequences, is proposed. String matching is performed using different block lengths provided by the perfect hash function instead of using the fixed block length as in the traditional Wu-Manber algorithm. The proposed approach has been compared with E. Coli and Human Chromosome1 datasets, frequently used in the literature, using multiple exact string matching algorithms. The proposed algorithm gives better results for performance metrics such as the average runtime, the average number of characters and hash comparisons.

2009 saw the first description of Candida auris, a yeast pathogen of humans. C. auris has since grown into a global problem in intensive care settings, where it causes systemic infections in patients with underlying health issues. Recent whole-genome sequencing has discerned five C. auris clades with distinct phenotypic features which display genomic divergence on a DNA sequence and a chromosome structure level. In the absence of sexual reproduction in C. auris, the mechanism(s) behind the rapid genomic evolution of this emerging killer yeast has remained obscure. Yet, one important bit of information about chromosome organization was missing, the identification of the centromeres.

Molecular variation of the cytochrome b DNA and protein sequences in Phytoseiulus macropilis and P. persimilis (Acari: Phytoseiidae) reflect population differentiation

Several phytoseiid mite species are important natural enemies used in biological control strategies. In the present study, Cytb mtDNA sequences of various populations of two species, Phytoseiulus macropolis and P. persimilis, were compared to determine whether the specimens collected in Brazil could belong to P. persimilis as this latter species is reported in South America but not in Brazil. The Cytb marker was used because of its high evolution rate, assumed to capture intraspecific variation. No overlap between intra- and interspecific distances was observed but the distances were quite low for interspecific variation.

This can be due to the particular biology of Phytoseiulus species and this shows the difficulty to apply a universal threshold in genetic distances to conclude about the existence of one or several species. Cytb mtDNA sequences were also considered to assess intraspecific variation. The DNA sequences of P. persimilis populations were very similar, probably because they all originated from the West Palearctic region or because of a prevalence of commercialized specimens in natura. For P. macropilis, higher genetic distances were observed and differentiation was noted according to geographic location and, to a smaller extent, pyrethroid resistance.

The WM-q multiple exact string matching algorithm for DNA sequences

To determine how DNA variation might impact the protein function (CytB fragment considered), the amino acid compositions of the populations studied were compared. No diagnostic mutation was observed between pyrethroid resistant and susceptible populations, whereas four mutations were identified between populations of P. macropilis separated by 1300 km (different climatic conditions). The impact of such mutations is discussed but knowledge is scarce, which makes it difficult to root testable hypotheses. The protein analysis clearly opens new perspectives in Phytoseiidae studies.

Characterization of genomic DNA sequence of the candidate gene for FB_Mfu10 associated with fire blight resistance in Malus species

 The proposed candidate gene underlying the Malus fusca fire blight resistance locus on chromosome 10 was previously predicted to possess 880 amino acids and 8 exons. Eight base pair (8 bp) insertion/deletion in the first exon potentially distinguished resistant genotypes from susceptible ones. This study aimed at analyzing the candidate gene sequence in another set of original resistant and susceptible progeny, characterizing the sequence in a transgenic line transformed with the candidate gene under its own native promoter, as well as deciphering the potential genomic differences between this candidate gene and its homolog in the ‘Golden Delicious’ doubled haploid genome (GDDH13).

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LncRNA Profiler Complete qPCR Array Kit (cDNA synthesis kit, qPCR array and SYBR Green reagent) 20 profiles

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qPCR Master Mix E1 (SafeLine: EvaGreen, dUTP), packed in 1,25 ml vials

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qPCR Master Mix E1 (SafeLine: EvaGreen, dUTP), packed in 1,25 ml vials

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qPCR Master Mix DLP2 (SafeLine: dUTP, UNG), packed in 1,25 ml vials

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HotTaq Probe qPCR Mix (ROX)

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amfiSure Advanced PCR Master Mix

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2 × Vazyme LAmp Master Mix

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AceQ U+ Probe Master Mix

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amfiRivert cDNA Synthesis Master Mix

R5101-050 50 rxns
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qPCR Master Mix E2 (SafeLine: EvaGreen, dUTP, UNG), packed in 1,25 ml vials

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qPCR Master Mix E2 (SafeLine: EvaGreen, dUTP, UNG), packed in 1,25 ml vials

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SYBR Green I Nucleic Acid Gel Stain

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Eztime Real - time PCRPremix 2x,SYBR Green

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Top Green qPCR SuperMix (+Dye II)

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Tip Green qPCR SuperMix (+Dye II)

20-abx098891
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HotTaq Probe qPCR Mix (no ROX)

BT11002 250rxn
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HotTaq EvaGreen qPCR Mix (no ROX)

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qPCR Master Mix DLP3 (SafeLine: dUTP, 500 nM ROX), packed in 1,25 ml vials

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ExoELISA-ULTRA Complete Kit (CD63 detection)

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Fast Probe Master Mix (200 rxn)

31005 2x1ML
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Pfu 2x Master Mix - 200 Reactions

3326 1/EA
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2 × Taq Master Mix (Dye Plus)

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2 × Taq Master Mix (Dye Plus)

P112-02 15 ml
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P112-03 50 ml
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Accuris Hot Start Taq Master Mix

PR1001-HS-1000 1 PC
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Accuris Hot Start Taq Master Mix

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Sequences of amplicons of part of the candidate gene amplified in two progenies that showed resistant and susceptible fire blight phenotypes, confirmed the 8 bp insertion that distinguishes susceptible and resistant progenies. The transgenic line was positive for the candidate gene sequence, confirming a successful transfer into the background of apple cultivar ‘Pinova’, and possessed the same genomic sequence as the progeny with a resistant phenotype. Sequence analysis showed that the homolog gene on GDDH13 possesses a significant 18 bp deletion in exon 1 leading to a difference of 15 amino acid from the protein sequence of the candidate gene.

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