LNCediting: a database for functional effects of RNA editing in lncRNAs
RNA editing is a widespread post-transcriptional mechanism that can make a single base change on specific nucleotide sequence in an RNA transcript. RNA editing events can result in missense codon changes and modulation of alternative splicing in mRNA, and modification of regulatory RNAs and their binding sites in noncoding RNAs. Recent computational studies accurately detected more than 2 million A-to-I RNA editing sites from next-generation sequencing (NGS). However, the vast majority of these RNA editing sites have unknown functions and are in noncoding regions of the genome. To provide a useful resource for the function...
Source: Nucleic Acids Research - January 2, 2017 Category: Research Authors: Gong, J., Liu, C., Liu, W., Xiang, Y., Diao, L., Guo, A.-Y., Han, L. Tags: Database Issue Source Type: research
LincSNP 2.0: an updated database for linking disease-associated SNPs to human long non-coding RNAs and their TFBSs
We describe LincSNP 2.0 (http://bioinfo.hrbmu.edu.cn/LincSNP), an updated database that is used specifically to store and annotate disease-associated single nucleotide polymorphisms (SNPs) in human long non-coding RNAs (lncRNAs) and their transcription factor binding sites (TFBSs). In LincSNP 2.0, we have updated the database with more data and several new features, including (i) expanding disease-associated SNPs in human lncRNAs; (ii) identifying disease-associated SNPs in lncRNA TFBSs; (iii) updating LD-SNPs from the 1000 Genomes Project; and (iv) collecting more experimentally supported SNP-lncRNA-disease associations. ...
Source: Nucleic Acids Research - January 2, 2017 Category: Research Authors: Ning, S., Yue, M., Wang, P., Liu, Y., Zhi, H., Zhang, Y., Zhang, J., Gao, Y., Guo, M., Zhou, D., Li, X., Li, X. Tags: Database Issue Source Type: research
L1Base 2: more retrotransposition-active LINE-1s, more mammalian genomes
LINE-1 (L1) insertions comprise as much as 17% of the human genome sequence, and similar proportions have been recorded for other mammalian species. Given the established role of L1 retrotransposons in shaping mammalian genomes, it becomes an important task to track and annotate the sources of this activity: full length elements, able to encode the cis and trans acting components of the retrotransposition machinery. The L1Base database (http://l1base.charite.de) contains annotated full-length sequences of LINE-1 transposons including putatively active L1s. For the new version of L1Base, a LINE-1 annotation tool, L1Xplorer,...
Source: Nucleic Acids Research - January 2, 2017 Category: Research Authors: Penzkofer, T., Jäger, M., Figlerowicz, M., Badge, R., Mundlos, S., Robinson, P. N., Zemojtel, T. Tags: Database Issue Source Type: research
GTRD: a database of transcription factor binding sites identified by ChIP-seq experiments
GTRD—Gene Transcription Regulation Database (http://gtrd.biouml.org)—is a database of transcription factor binding sites (TFBSs) identified by ChIP-seq experiments for human and mouse. Raw ChIP-seq data were obtained from ENCODE and SRA and uniformly processed: (i) reads were aligned using Bowtie2; (ii) ChIP-seq peaks were called using peak callers MACS, SISSRs, GEM and PICS; (iii) peaks for the same factor and peak callers, but different experiment conditions (cell line, treatment, etc.), were merged into clusters; (iv) such clusters for different peak callers were merged into metaclusters that were considered...
Source: Nucleic Acids Research - January 2, 2017 Category: Research Authors: Yevshin, I., Sharipov, R., Valeev, T., Kel, A., Kolpakov, F. Tags: Database Issue Source Type: research
GETPrime 2.0: gene- and transcript-specific qPCR primers for 13 species including polymorphisms
GETPrime (http://bbcftools.epfl.ch/getprime) is a database with a web frontend providing gene- and transcript-specific, pre-computed qPCR primer pairs. The primers have been optimized for genome-wide specificity and for allowing the selective amplification of one or several splice variants of most known genes. To ease selection, primers have also been ranked according to defined criteria such as genome-wide specificity (with BLAST), amplicon size, and isoform coverage. Here, we report a major upgrade (2.0) of the database: eight new species (yeast, chicken, macaque, chimpanzee, rat, platypus, pufferfish, and Anolis carolin...
Source: Nucleic Acids Research - January 2, 2017 Category: Research Authors: David, F. P. A., Rougemont, J., Deplancke, B. Tags: Database Issue Source Type: research
The eukaryotic promoter database in its 30th year: focus on non-vertebrate organisms
We present an update of the Eukaryotic Promoter Database EPD (http://epd.vital-it.ch), more specifically on the EPDnew division, which contains comprehensive organisms-specific transcription start site (TSS) collections automatically derived from next generation sequencing (NGS) data. Thanks to the abundant release of new high-throughput transcript mapping data (CAGE, TSS-seq, GRO-cap) the database could be extended to plant and fungal species. We further report on the expansion of the mass genome annotation (MGA) repository containing promoter-relevant chromatin profiling data and on improvements for the EPD entry viewers...
Source: Nucleic Acids Research - January 2, 2017 Category: Research Authors: Dreos, R., Ambrosini, G., Groux, R., Cavin Perier, R., Bucher, P. Tags: Database Issue Source Type: research
ChIPBase v2.0: decoding transcriptional regulatory networks of non-coding RNAs and protein-coding genes from ChIP-seq data
This study will greatly expand our understanding of the transcriptional regulations of ncRNAs and PCGs. (Source: Nucleic Acids Research)
Source: Nucleic Acids Research - January 2, 2017 Category: Research Authors: Zhou, K.-R., Liu, S., Sun, W.-J., Zheng, L.-L., Zhou, H., Yang, J.-H., Qu, L.-H. Tags: Database Issue Source Type: research
GenBank
® (www.ncbi.nlm.nih.gov/genbank/) is a comprehensive database that contains publicly available nucleotide sequences for 370 000 formally described species. These sequences are obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects, including whole genome shotgun (WGS) and environmental sampling projects. Most submissions are made using the web-based BankIt or the NCBI Submission Portal. GenBank staff assign accession numbers upon data receipt. Daily data exchange with the European Nucleotide Archive (ENA) and the DNA Data Bank of Japan (DDBJ) ensur...
Source: Nucleic Acids Research - January 2, 2017 Category: Research Authors: Benson, D. A., Cavanaugh, M., Clark, K., Karsch-Mizrachi, I., Lipman, D. J., Ostell, J., Sayers, E. W. Tags: Database Issue Source Type: research
DNA Data Bank of Japan
The DNA Data Bank of Japan (DDBJ) (http://www.ddbj.nig.ac.jp) has been providing public data services for thirty years (since 1987). We are collecting nucleotide sequence data from researchers as a member of the International Nucleotide Sequence Database Collaboration (INSDC, http://www.insdc.org), in collaboration with the US National Center for Biotechnology Information (NCBI) and European Bioinformatics Institute (EBI). The DDBJ Center also services Japanese Genotype-phenotype Archive (JGA), with the National Bioscience Database Center to collect human-subjected data from Japanese researchers. Here, we report our databa...
Source: Nucleic Acids Research - January 2, 2017 Category: Research Authors: Mashima, J., Kodama, Y., Fujisawa, T., Katayama, T., Okuda, Y., Kaminuma, E., Ogasawara, O., Okubo, K., Nakamura, Y., Takagi, T. Tags: Database Issue Source Type: research
The BIG Data Center: from deposition to integration to translation
Biological data are generated at unprecedentedly exponential rates, posing considerable challenges in big data deposition, integration and translation. The BIG Data Center, established at Beijing Institute of Genomics (BIG), Chinese Academy of Sciences, provides a suite of database resources, including (i) Genome Sequence Archive, a data repository specialized for archiving raw sequence reads, (ii) Gene Expression Nebulas, a data portal of gene expression profiles based entirely on RNA-Seq data, (iii) Genome Variation Map, a comprehensive collection of genome variations for featured species, (iv) Genome Warehouse, a centra...
Source: Nucleic Acids Research - January 2, 2017 Category: Research Authors: BIG Data Center Members Tags: Database Issue Source Type: research
Database Resources of the National Center for Biotechnology Information
The National Center for Biotechnology Information (NCBI) provides a large suite of online resources for biological information and data, including the GenBank® nucleic acid sequence database and the PubMed database of citations and abstracts for published life science journals. The Entrez system provides search and retrieval operations for most of these data from 37 distinct databases. The E-utilities serve as the programming interface for the Entrez system. Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. New resources released in the pa...
Source: Nucleic Acids Research - January 2, 2017 Category: Research Authors: NCBI Resource Coordinators Tags: Database Issue Source Type: research
The 24th annual Nucleic Acids Research database issue: a look back and upcoming changes
This year's Database Issue of Nucleic Acids Research contains 152 papers that include descriptions of 54 new databases and update papers on 98 databases, of which 16 have not been previously featured in NAR. As always, these databases cover a broad range of molecular biology subjects, including genome structure, gene expression and its regulation, proteins, protein domains, and protein–protein interactions. Following the recent trend, an increasing number of new and established databases deal with the issues of human health, from cancer-causing mutations to drugs and drug targets. In accordance with this trend, three...
Source: Nucleic Acids Research - January 2, 2017 Category: Research Authors: Galperin, M. Y., Fernandez-Suarez, X. M., Rigden, D. J. Tags: Database Issue Source Type: research
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Source: Nucleic Acids Research - January 2, 2017 Category: Research Tags: Front-Matter/Back-Matter Source Type: research
Nucleic Acids Research: Editorial Board
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Source: Nucleic Acids Research - January 2, 2017 Category: Research Tags: Front-Matter/Back-Matter Source Type: research
Nucleic Acids Research: VOLUME 45 DATABASE ISSUE JANUARY 4 2017
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Source: Nucleic Acids Research - January 2, 2017 Category: Research Tags: Front-Matter/Back-Matter Source Type: research
