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Limited By:	Author = Kiran, Anmol M.;

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Darned in 2013: inclusion of model organisms and linking with Wikipedia (2013)

Kiran, Anmol M.; O'Mahony, John J.; Sanjeev, Komal; Baranov, Pavel V.

Darned in 2013: inclusion of model organisms and linking with Wikipedia (2013)

Kiran, Anmol M.; O'Mahony, John J.; Sanjeev, Komal; Baranov, Pavel V.

Abstract:

DARNED (DAtabase of RNA EDiting, available at http://darned.ucc.ie) is a centralized repository of reference genome coordinates corresponding to RNA nucleotides having altered templated identities in the process of RNA editing. The data in DARNED are derived from published datasets of RNA editing events. RNA editing instances have been identified with various methods, such as bioinformatics screenings, deep sequencing and/or biochemical techniques. Here we report our current progress in the development and expansion of the DARNED. In addition to novel database features the DARNED update describes inclusion of Drosophila melanogaster and Mus musculus RNA editing events and the launch of a community-based annotation in the RNA WikiProject.

http://hdl.handle.net/10468/5021

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Evidence of efficient stop codon readthrough in four mammalian genes (2014)

Loughran, Gary; Chou, Ming-Yuan; Ivanov, Ivaylo P.; Jungreis, Irwin; Kellis, Manolis; K...

Evidence of efficient stop codon readthrough in four mammalian genes (2014)

Loughran, Gary; Chou, Ming-Yuan; Ivanov, Ivaylo P.; Jungreis, Irwin; Kellis, Manolis; Kiran, Anmol M.; Baranov, Pavel V.; Atkins, John F.

Abstract:

Stop codon readthrough is used extensively by viruses to expand their gene expression. Until recent discoveries in Drosophila, only a very limited number of readthrough cases in chromosomal genes had been reported. Analysis of conserved protein coding signatures that extend beyond annotated stop codons identified potential stop codon readthrough of four mammalian genes. Here we use a modified targeted bioinformatic approach to identify a further three mammalian readthrough candidates. All seven genes were tested experimentally using reporter constructs transfected into HEK-293T cells. Four displayed efficient stop codon readthrough, and these have UGA immediately followed by CUAG. Comparative genomic analysis revealed that in the four readthrough candidates containing UGA-CUAG, this motif is conserved not only in mammals but throughout vertebrates with the first six of the seven nucleotides being universally conserved. The importance of the CUAG motif was confirmed using a systemati...

http://hdl.handle.net/10468/5016

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GWIPS-viz: development of a ribo-seq genome browser (2014)

Michel, Audrey M.; Fox, Gearoid; Kiran, Anmol M.; De Bo, Christof; O'Connor, Patri...

GWIPS-viz: development of a ribo-seq genome browser (2014)

Michel, Audrey M.; Fox, Gearoid; Kiran, Anmol M.; De Bo, Christof; O'Connor, Patrick B. F.; Heaphy, Stephen M.; Mullan, James P. A.; Donohue, Claire A.; Higgins, Desmond G.; Baranov, Pavel V.

Abstract:

We describe the development of GWIPS-viz (http://gwips.ucc.ie), an online genome browser for viewing ribosome profiling data. Ribosome profiling (ribo-seq) is a recently developed technique that provides genome-wide information on protein synthesis (GWIPS) in vivo. It is based on the deep sequencing of ribosome-protected messenger RNA (mRNA) fragments, which allows the ribosome density along all mRNA transcripts present in the cell to be quantified. Since its inception, ribo-seq has been carried out in a number of eukaryotic and prokaryotic organisms. Owing to the increasing interest in ribo-seq, there is a pertinent demand for a dedicated ribo-seq genome browser. GWIPS-viz is based on The University of California Santa Cruz (UCSC) Genome Browser. Ribo-seq tracks, coupled with mRNA-seq tracks, are currently available for several genomes: human, mouse, zebrafish, nematode, yeast, bacteria (Escherichia coli K12, Bacillus subtilis), human cytomegalovirus and bacteriophage lambda. Our o...

http://hdl.handle.net/10468/5018

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