01.01.2012 | Madupu, Ramana; Richter, Alexander; Dodson, Robert J.; Brinkac, Lauren; Harkins, Derek; Durkin, Scott; Shrivastava, ..., Nucleic Acids Research, 2012

CharProtDB (http://www.jcvi.org/charprotdb/) is a curated database of biochemically characterized proteins. It provides a source of direct rather than transitive assignments of function, designed to support automated annotation pipelines. The initial data set in CharProtDB was collected ...

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01.01.2012 | Thakur, Nishant; Qureshi, Abid; Kumar, Manoj, Nucleic Acids Research, 2012

RNAi technology has been emerging as a potential modality to inhibit viruses during past decade. In literature a few siRNA databases have been reported that focus on targeting human and mammalian genes but experimentally validated viral siRNA databases are lacking. We have developed ...

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01.01.2012 | Vergoulis, Thanasis; Vlachos, Ioannis S.; Alexiou, Panagiotis; Georgakilas, George; Maragkakis, Manolis; Reczko, Mar ..., Nucleic Acids Research, 2012

As the relevant literature and the number of experiments increase at a super linear rate, databases that curate and collect experimentally verified microRNA (miRNA) targets have gradually emerged. These databases attempt to provide efficient access to this wealth of experimental data, which ...

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01.01.2012 | Ziebarth, Jesse D.; Bhattacharya, Anindya; Chen, Anlong; Cui, Yan, Nucleic Acids Research, 2012

The polymorphism in microRNA target site (PolymiRTS) database aims to identify single-nucleotide polymorphisms (SNPs) that affect miRNA targeting in human and mouse. These polymorphisms can disrupt the regulation of gene expression by miRNAs and are candidate genetic variants responsible for ...

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01.01.2012 | Bu, Dechao; Yu, Kuntao; Sun, Silong; Xie, Chaoyong; Skogerbø, Geir; Miao, Ruoyu; Xiao, Hui; Liao, Qi; Luo, Haitao; Z ..., Nucleic Acids Research, 2012

Facilitated by the rapid progress of high-throughput sequencing technology, a large number of long noncoding RNAs (lncRNAs) have been identified in mammalian transcriptomes over the past few years. LncRNAs have been shown to play key roles in various biological processes such as imprinting ...

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01.01.2012 | Ott, Alban; Idali, Anouar; Marchais, Antonin; Gautheret, Daniel, Nucleic Acids Research, 2012

Nucleic acid phylogenetic profiling (NAPP) classifies coding and non-coding sequences in a genome according to their pattern of conservation across other genomes. This procedure efficiently distinguishes clusters of functional non-coding elements in bacteria, particularly small RNAs and ...

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01.01.2012 | Szcześniak, Michał Wojciech; Deorowicz, Sebastian; Gapski, Jakub; Kaczyński, Łukasz; Makałowska, Izabela, Nucleic Acids Research, 2012

Despite accumulating data on animal and plant microRNAs and their functions, existing public miRNA resources usually collect miRNAs from a very limited number of species. A lot of microRNAs, including those from model organisms, remain undiscovered. As a result there is a continuous need to ...

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01.01.2012 | Candales, Manuel A.; Duong, Adrian; Hood, Keyar S.; Li, Tony; Neufeld, Ryan A. E.; Sun, Runda; McNeil, Bonnie A.; Wu ..., Nucleic Acids Research, 2012

The Database for Bacterial Group II Introns (http://webapps2.ucalgary.ca/~groupii/index.html#) provides a catalogue of full-length, non-redundant group II introns present in bacterial DNA sequences in GenBank. The website is divided into three sections. The first section provides general ...

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01.01.2012 | Anders, Gerd; Mackowiak, Sebastian D.; Jens, Marvin; Maaskola, Jonas; Kuntzagk, Andreas; Rajewsky, Nikolaus; Landtha ..., Nucleic Acids Research, 2012

In animals, RNA binding proteins (RBPs) and microRNAs (miRNAs) post-transcriptionally regulate the expression of virtually all genes by binding to RNA. Recent advances in experimental and computational methods facilitate transcriptome-wide mapping of these interactions. It is thought that ...

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01.01.2012 | de Boer, Carl G.; Hughes, Timothy R., Nucleic Acids Research, 2012

The yeast Saccharomyces cerevisiae is a prevalent system for the analysis of transcriptional networks. As a result, multiple DNA-binding sequence specificities (motifs) have been derived for most yeast transcription factors (TFs). However, motifs from different studies are often inconsistent ...

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