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Limited By:	Subject = Nucleotide sequence;

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Displaying Results 1 - 4 of 4 on page 1 of 1

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Optimal Probe Length Varies for Targets with High Sequence Variation: Implications for Probe Library Design for Resequencing Highly Variable Genes (2012)

Haslam, Niall J.; Whiteford, Nava E.; Weber, Gerald; Prügel-Bennett, Adam; Essex, Jonat...

Optimal Probe Length Varies for Targets with High Sequence Variation: Implications for Probe Library Design for Resequencing Highly Variable Genes (2012)

Haslam, Niall J.; Whiteford, Nava E.; Weber, Gerald; Prügel-Bennett, Adam; Essex, Jonathan W.; Neylon, Cameron

Abstract:

Sequencing by hybridisation is an effective method for obtaining large amounts of DNA sequence information at low cost. The efficiency of SBH depends on the design of the probe library to provide the maximum information for minimum cost. Long probes provide a higher probability of non-repeated sequences but lead to an increase in the number of probes required whereas short probes may not provide unique sequence information due to repeated sequences. We have investigated the effect of probe length, use of reference sequences, and thermal filtering on the design of probe libraries for several highly variable target DNA sequences. Results We designed overlapping probe libraries for a range of highly variable drug target genes based on known sequence information and develop a formal terminology to describe probe library design. We find that for some targets these libraries can provide good coverage of a previously unseen target whereas for others the coverage is less than...

http://hdl.handle.net/10197/3945

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Role of Genomics and RNA-seq in Studies of Fungal Virulence (2012)

Riccombeni, Alessandro; Butler, Geraldine

Role of Genomics and RNA-seq in Studies of Fungal Virulence (2012)

Riccombeni, Alessandro; Butler, Geraldine

Abstract:

Since its introduction in the last decade, massive parallel sequencing, or “next-generation sequencing”, has revolutionized our access to genomic information, providing accurate data with increasingly higher yields and lower costs with respect to first-generation technology. Massive parallel sequencing of cDNA, or RNA-seq, is progressively replacing array-based technology as the method of choice for transcriptomics. This review describes some of the most recent applications of next-generation sequencing technology to the study of pathogenic fungi, including Candida, Aspergillus and Cryptococcus species. Several integrated approaches illustrate the power and accuracy of RNA-seq for studying the biology of human fungal pathogens. In addition, the lack of consistency in data analysis is discussed.
Author has checked copyright
DG - 10/10/2012
Item not published yet and only available online as part of "Online First" feature. I'm not sure when it's due to ...

http://hdl.handle.net/10197/3865

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Role of Genomics and RNA-seq in Studies of Fungal Virulence (2012)

Riccombeni, Alessandro; Butler, Geraldine

Role of Genomics and RNA-seq in Studies of Fungal Virulence (2012)

Riccombeni, Alessandro; Butler, Geraldine

Abstract:

Since its introduction in the last decade, massive parallel sequencing, or "next-generation sequencing", has revolutionized our access to genomic information, providing accurate data with increasingly higher yields and lower costs with respect to first-generation technology. Massive parallel sequencing of cDNA, or RNA-seq, is progressively replacing array-based technology as the method of choice for transcriptomics. This review describes some of the most recent applications of next-generation sequencing technology to the study of pathogenic fungi, including Candida, Aspergillus and Cryptococcusspecies. Several integrated approaches illustrate the power and accuracy of RNA-seq for studying the biology of human fungal pathogens. In addition, the lack of consistency in data analysis is discussed.
Copyright: "It is fully accessible to all users at libraries and institutions that have purchased a SpringerLink license. If your article is published under one of our Open ...

http://hdl.handle.net/10197/3934

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Stimulation of stop codon readthrough: frequent presence of an extended 3' RNA structural element (2011)

Firth, Andrew E.; Wills, Norma M.; Gesteland, Raymond F.; Atkins, John F.

Stimulation of stop codon readthrough: frequent presence of an extended 3' RNA structural element (2011)

Firth, Andrew E.; Wills, Norma M.; Gesteland, Raymond F.; Atkins, John F.

Abstract:

In Sindbis, Venezuelan equine encephalitis and related alphaviruses, the polymerase is translated as a fusion with other non-structural proteins via readthrough of a UGA stop codon. Surprisingly, earlier work reported that the signal for efficient readthrough comprises a single cytidine residue 3'-adjacent to the UGA. However, analysis of variability at synonymous sites revealed strikingly enhanced conservation within the similar to 150 nt 3'-adjacent to the UGA, and RNA folding algorithms revealed the potential for a phylogenetically conserved stem-loop structure in the same region. Mutational analysis of the predicted structure demonstrated that the stem-loop increases readthrough by up to 10-fold. The same computational analysis indicated that similar RNA structures are likely to be relevant to readthrough in certain plant virus genera, notably Furovirus, Pomovirus, Tobravirus, Pecluvirus and Benyvirus, as well as the Drosophilia gene kelch. These results suggest that 3...

http://hdl.handle.net/10468/5023

Displaying Results 1 - 4 of 4 on page 1 of 1