Research Topics
| Andrew E FirthSummaryAffiliation: University College Cork Country: Ireland Publications
| Collaborators
|
Detail Information
Publications
Detecting overlapping coding sequences with pairwise alignmentsAndrew E Firth
Department of Biochemistry, University of Otago, P.O. Box 56, Dunedin, New Zealand
Bioinformatics 21:282-92. 2005..AVAILABILITY: Programs may be obtained from the authors. SUPPLEMENTARY INFORMATION: http://biochem.otago.ac.nz/double.html...- Evidence for ribosomal frameshifting and a novel overlapping gene in the genomes of insect-specific flavivirusesAndrew E Firth
Biosciences Institute, University College Cork, Cork, Ireland
Virology 399:153-66. 2010.... - HBVRegDB: annotation, comparison, detection and visualization of regulatory elements in hepatitis B virus sequencesNattanan Panjaworayan
Department of Biochemistry, University of Otago, Dunedin, New Zealand
Virol J 4:136. 2007..2 kb) but contain multiple layers of functional regulatory elements in addition to coding regions. Key regions are subject to purifying selection, as mutations in these regions will produce non-functional viruses... - Analysis of the coding potential of the partially overlapping 3' ORF in segment 5 of the plant fijivirusesAndrew E Firth
Biosciences Institute, University College Cork, Cork, Ireland
Virol J 6:32. 2009..Possible translation mechanisms for this unusually positioned ORF are discussed... - Discovery of frameshifting in Alphavirus 6K resolves a 20-year enigmaAndrew E Firth
Biosciences Institute, University College Cork, Cork, Ireland
Virol J 5:108. 2008..In protein gels, 6K migrates as a doublet--a result that, to date, has been attributed to differing degrees of acylation. Nonetheless, despite many years of research, its role is still relatively poorly understood... - Bioinformatic analysis suggests that a conserved ORF in the waikaviruses encodes an overlapping geneAndrew E Firth
Biosciences Institute, University College Cork, Cork, Ireland
Arch Virol 153:1379-83. 2008..The ORF overlaps the polyprotein ORF but is in the +1 reading frame. Here, we describe the bioinformatic analysis... - Bioinformatic analysis suggests that the Cypovirus 1 major core protein cistron harbours an overlapping geneAndrew E Firth
Biosciences Institute, University College Cork, Cork, Ireland
Virol J 5:62. 2008..The ORFX amino acid sequences are hydrophilic and basic, with between 12 and 16 Arg/Lys residues in each though, at 7.5-10.2 kDa, the putative ORFX product is too small to appear on typical published protein gels... - Bioinformatic analysis suggests that the Orbivirus VP6 cistron encodes an overlapping geneAndrew E Firth
Department of Biochemistry, Biosciences Institute, University College Cork, Cork, Ireland
Virol J 5:48. 2008..These viruses have linear dsRNA genomes divided into ten segments, all of which have previously been assumed to be monocistronic... - A case for a CUG-initiated coding sequence overlapping torovirus ORF1a and encoding a novel 30 kDa productAndrew E Firth
Biosciences Institute, University College Cork, Cork, Ireland
Virol J 6:136. 2009..We propose that the new ORF utilizes a non-AUG initiation codon--namely a conserved CUG codon in a strong Kozak context--upstream of the ORF1a AUG initiation codon, resulting in a novel 258 amino acid protein, dubbed '30K'... - Bioinformatic evidence for a stem-loop structure 5'-adjacent to the IGR-IRES and for an overlapping gene in the bee paralysis dicistrovirusesAndrew E Firth
Biosciences Institute, University College Cork, Cork, Ireland
Virol J 6:193. 2009..We also identify a potential 14-18 bp RNA stem-loop structure 5'-adjacent to the IGR-IRES. We discuss potential translation initiation mechanisms for the novel ORF in the context of the IGR-IRES and 5'-adjacent stem-loop... - Evidence for a novel coding sequence overlapping the 5'-terminal approximately 90 codons of the gill-associated and yellow head okavirus envelope glycoprotein geneAndrew E Firth
Biosciences Institute, University College Cork, Cork, Ireland
Virol J 6:222. 2009..We propose that translation of the new ORF initiates at a conserved AUG codon separated by just 2 nt from the ORF3 AUG initiation codon, resulting in a novel 86 amino acid protein... - Candidates in Astroviruses, Seadornaviruses, Cytorhabdoviruses and Coronaviruses for +1 frame overlapping genes accessed by leaky scanningAndrew E Firth
Biosciences Institute, University College Cork, Cork, Ireland
Virol J 7:17. 2010..RESULTS: Overlapping gene predictions are presented for the astroviruses, seadornaviruses, cytorhabdoviruses and coronaviruses (families Astroviridae, Reoviridae, Rhabdoviridae and Coronaviridae, respectively)... - A conserved predicted pseudoknot in the NS2A-encoding sequence of West Nile and Japanese encephalitis flaviviruses suggests NS1' may derive from ribosomal frameshiftingAndrew E Firth
Biosciences Institute, University College Cork, Cork, Ireland
Virol J 6:14. 2009..We hypothesize that this may explain the origin of the previously identified NS1 'extension' protein in JEV-group flaviviruses, known as NS1'... - Ribosomal frameshifting into an overlapping gene in the 2B-encoding region of the cardiovirus genomeGary Loughran
Biosciences Institute, University College Cork, Cork, Ireland
Proc Natl Acad Sci U S A 108:E1111-9. 2011..Unlike previous cases of programmed -1 frameshifting, here frameshifting is modulated by virus infection, thus suggesting a novel regulatory role for frameshifting in these viruses... - Programmed ribosomal frameshifting in the expression of the regulator of intestinal stem cell proliferation, adenomatous polyposis coli (APC)Pavel V Baranov
Biochemistry Department, University College Cork, Cork, Ireland
RNA Biol 8:637-47. 2011..Three other proposed PRF candidates (Xbp1, CG32736, CG14047) with switches in conservation of reading frames are likely explained by mechanisms other than PRF... - A pilot study of bacterial genes with disrupted ORFs reveals a surprising profusion of protein sequence recoding mediated by ribosomal frameshifting and transcriptional realignmentVirag Sharma
Department of Biochemistry, University College Cork, Cork, Ireland
Mol Biol Evol 28:3195-211. 2011..In addition to the identification of a large number of recoded genes, a surprising observation is that nearly half of them are expressed via PTR-a mechanism that, in contrast to PRF, has not yet received substantial attention... - An overlapping essential gene in the PotyviridaeBetty Y W Chung
Biosciences Institute, University College Cork, Cork, Ireland
Proc Natl Acad Sci U S A 105:5897-902. 2008.... - Recode-2: new design, new search tools, and many more genesMichael Bekaert
School of Biology and Environmental Science, University College Dublin, Biosciences Institute, University College Cork, Ireland
Nucleic Acids Res 38:D69-74. 2010..Recode-2 is available at http://recode.ucc.ie... - Identification of evolutionarily conserved non-AUG-initiated N-terminal extensions in human coding sequencesIvaylo P Ivanov
Biosciences Institute, University College Cork, Cork, Ireland
Nucleic Acids Res 39:4220-34. 2011..In several instances, we have been able to obtain independent experimental evidence of the expression of non-AUG-initiated products from the previously published literature and ribosome profiling data... - Frameshifting in alphaviruses: a diversity of 3' stimulatory structuresBetty Y W Chung
Biosciences Institute, University College Cork, Cork, Ireland
J Mol Biol 397:448-56. 2010..The analysis, both experimental and bioinformatic, significantly expands the known repertoire of -1 frameshifting stimulators in mammalian and insect systems... - Effect of 5'UTR introns on gene expression in Arabidopsis thalianaBetty Y W Chung
Biochemistry Department, University of Otago, Dunedin, New Zealand
BMC Genomics 7:120. 2006..Alignment of the whole genome and expressed sequence tags (ESTs) of the model plant Arabidopsis thaliana has identified introns residing in both coding and non-coding regions of the genome... - Recurrent emergence of catalytically inactive ornithine decarboxylase homologous forms that likely have regulatory functionIvaylo P Ivanov
Biosciences Institute, University College Cork, Ireland
J Mol Evol 70:289-302. 2010.... - GLUE-IT and PEDEL-AA: new programmes for analyzing protein diversity in randomized librariesAndrew E Firth
Biosciences Institute, University College Cork, Cork, Ireland
Nucleic Acids Res 36:W281-5. 2008..Output includes amino acid completeness and diversity statistics, and the number and length distribution of sequences truncated by premature termination codons. The web interfaces are available at http://guinevere.otago.ac.nz/stats.html... - Detecting overlapping coding sequences in virus genomesAndrew E Firth
Department of Biochemistry, University of Otago, PO Box 56, Dunedin, New Zealand
BMC Bioinformatics 7:75. 2006..g. frameshifting, stop codon read-through, leaky-scanning and internal ribosome entry sites--which can conceal potentially coding open reading frames (ORFs)... - Strategies and computational tools for improving randomized protein librariesWayne M Patrick
Center for Fundamental and Applied Molecular Evolution, Emory University, 1510 Clifton Road, Atlanta GA 30322, USA
Biomol Eng 22:105-12. 2005..In addition, we review recent methodological developments that facilitate the construction of unbiased libraries, which are inherently more diverse than biased libraries and therefore more likely to yield improved variants... - Statistics of protein library constructionAndrew E Firth
Department of Biochemistry, University of Otago, PO Box 56, Dunedin, New Zealand
Bioinformatics 21:3314-5. 2005..otago.ac.nz/stats.html. SUPPLEMENTARY INFORMATION: Complete mathematical notes, model assumptions and justification, users' guide and worked examples at above website...