In silico microarray probe design for diagnosis of multiple pathogens

Satya, Ravi Vijaya; Zavaljevski, Nela; Kumar, Kamal; Bode, Elizabeth; Padilla, Susana; Wasieloski, Leonard P.; Geyer, Jeanne A.; Reifman, Jaques

doi:10.1186/1471-2164-9-496

Cited by 16 publications

(9 citation statements)

References 24 publications

(29 reference statements)

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“…Several high-throughput applications have been developed recently to design diagnostic primers using the whole genome sequence information including KPATH, Insignia, TOFI, and TOPSI [ 34 - 40 ]. Among them, KPATH, Insignia, and TOPSI have the potential to be used for design of real-time PCR primers for qRT-PCR based assays for Las, whereas TOFI is used to design signatures for microarray-based assays.…”

Section: Resultsmentioning

confidence: 99%

Repertoire of novel sequence signatures for the detection of Candidatus Liberibacter asiaticus by quantitative real-time PCR

et al. 2014

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BackgroundHuanglongbing (HLB) or citrus greening is a devastating disease of citrus. The gram-negative bacterium Candidatus Liberibacter asiaticus (Las) belonging to the α-proteobacteria is responsible for HLB in North America as well as in Asia. Currently, there is no cure for this disease. Early detection and quarantine of Las-infected trees are important management strategies used to prevent HLB from invading HLB-free citrus producing regions. Quantitative real-time PCR (qRT-PCR) based molecular diagnostic assays have been routinely used in the detection and diagnosis of Las. The oligonucleotide primer pairs based on conserved genes or regions, which include 16S rDNA and the β-operon, have been widely employed in the detection of Las by qRT-PCR. The availability of whole genome sequence of Las now allows the design of primers beyond the conserved regions for the detection of Las explicitly.ResultsWe took a complimentary approach by systematically screening the genes in a genome-wide fashion, to identify the unique signatures that are only present in Las by an exhaustive sequence based similarity search against the nucleotide sequence database. Our search resulted in 34 probable unique signatures. Furthermore, by designing the primer pair specific to the identified signatures, we showed that most of our primer sets are able to detect Las from the infected plant and psyllid materials collected from the USA and China by qRT-PCR. Overall, 18 primer pairs of the 34 are found to be highly specific to Las with no cross reactivity to the closely related species Ca. L. americanus (Lam) and Ca. L. africanus (Laf).ConclusionsWe have designed qRT-PCR primers based on Las specific genes. Among them, 18 are suitable for the detection of Las from Las-infected plant and psyllid samples. The repertoire of primers that we have developed and characterized in this study enhanced the qRT-PCR based molecular diagnosis of HLB.

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Section: Resultsmentioning

confidence: 99%

Repertoire of novel sequence signatures for the detection of Candidatus Liberibacter asiaticus by quantitative real-time PCR

et al. 2014

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“…Such variation can be accounted for by between-sequences differences and by differences in the genome G + C content [24]. …”

Section: Discussionmentioning

confidence: 99%

“…The number of virtual hybridization signals obtained with the UFC-13 has a very close relationship, but with significant variation, with the size of the genome of the organisms. Such variation can be accounted for by between-sequences differences and by differences in the genome G + C content [ 24 ].…”

Section: Discussionmentioning

confidence: 99%

In Silico Genomic Fingerprints of the Bacillus anthracis Group Obtained by Virtual Hybridization

et al. 2015

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In this study we evaluate the capacity of Virtual Hybridization to identify between highly related bacterial strains. Eight genomic fingerprints were obtained by virtual hybridization for the Bacillus anthracis genome set, and a set of 15,264 13-nucleotide short probes designed to produce genomic fingerprints unique for each organism. The data obtained from each genomic fingerprint were used to obtain hybridization patterns simulating a DNA microarray. Two virtual hybridization methods were used: the Direct and the Extended method to identify the number of potential hybridization sites and thus determine the minimum sensitivity value to discriminate between genomes with 99.9% similarity. Genomic fingerprints were compared using both methods and phylogenomic trees were constructed to verify that the minimum detection value is 0.000017. Results obtained from the genomic fingerprints suggest that the distribution in the trees is correct, as compared to other taxonomic methods. Specific virtual hybridization sites for each of the genomes studied were also identified.

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“…TOFI is typically used to design fingerprints for a single genome. An enhanced multiple-genome pipeline presented by Satya et al allows for efficient design of microarray probes common to groups of target genomes[ 11 ]. Insignia is web-based tool for identifying genomic signatures that are perfectly conserved by all target genomes and absent from all background genomes based on databases of bacterial and viral genomic sequences, which comprise over 8300 distinct organisms[ 12 , 13 ].…”

Section: Introductionmentioning

confidence: 99%

An algorithm of discovering signatures from DNA databases on a computer cluster

Lee

Sheu

2014

BMC Bioinformatics

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BackgroundSignatures are short sequences that are unique and not similar to any other sequence in a database that can be used as the basis to identify different species. Even though several signature discovery algorithms have been proposed in the past, these algorithms require the entirety of databases to be loaded in the memory, thus restricting the amount of data that they can process. It makes those algorithms unable to process databases with large amounts of data. Also, those algorithms use sequential models and have slower discovery speeds, meaning that the efficiency can be improved.ResultsIn this research, we are debuting the utilization of a divide-and-conquer strategy in signature discovery and have proposed a parallel signature discovery algorithm on a computer cluster. The algorithm applies the divide-and-conquer strategy to solve the problem posed to the existing algorithms where they are unable to process large databases and uses a parallel computing mechanism to effectively improve the efficiency of signature discovery. Even when run with just the memory of regular personal computers, the algorithm can still process large databases such as the human whole-genome EST database which were previously unable to be processed by the existing algorithms.ConclusionsThe algorithm proposed in this research is not limited by the amount of usable memory and can rapidly find signatures in large databases, making it useful in applications such as Next Generation Sequencing and other large database analysis and processing. The implementation of the proposed algorithm is available athttp://www.cs.pu.edu.tw/~fang/DDCSDPrograms/DDCSD.htm.

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In silico microarray probe design for diagnosis of multiple pathogens

Cited by 16 publications

References 24 publications

Repertoire of novel sequence signatures for the detection of Candidatus Liberibacter asiaticus by quantitative real-time PCR

Repertoire of novel sequence signatures for the detection of Candidatus Liberibacter asiaticus by quantitative real-time PCR

In Silico Genomic Fingerprints of the Bacillus anthracis Group Obtained by Virtual Hybridization

An algorithm of discovering signatures from DNA databases on a computer cluster

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