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The UCSC Cancer Genomics Browser: update 2013.

Goldman, Mary Craft, Brian Swatloski, Teresa Ellrott, Kyle Cline, Melissa Diekhans, Mark Ma, Singer Wilks, Chris Stuart, Josh Haussler, David ...

Published in Nucleic acids research

The UCSC Cancer Genomics Browser (https://genome-cancer.ucsc.edu/) is a set of web-based tools to display, investigate and analyse cancer genomics data and its associated clinical information. The browser provides whole-genome to base-pair level views of several different types of genomics data, including some next-generation sequencing platforms. ...

tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA genes.

Lowe, Todd M Chan, Patricia P

Published in Nucleic acids research

High-throughput genome sequencing continues to grow the need for rapid, accurate genome annotation and tRNA genes constitute the largest family of essential, ever-present non-coding RNA genes. Newly developed tRNAscan-SE 2.0 has advanced the state-of-the-art methodology in tRNA gene detection and functional prediction, captured by rich new content ...

RBPmap: a web server for mapping binding sites of RNA-binding proteins.

Paz, Inbal Kosti, Idit Ares, Manuel Jr Cline, Melissa Mandel-Gutfreund, Yael

Published in Nucleic acids research

Regulation of gene expression is executed in many cases by RNA-binding proteins (RBPs) that bind to mRNAs as well as to non-coding RNAs. RBPs recognize their RNA target via specific binding sites on the RNA. Predicting the binding sites of RBPs is known to be a major challenge. We present a new webserver, RBPmap, freely accessible through the websi...

ENCODE data in the UCSC Genome Browser: year 5 update.

Rosenbloom, Kate R Sloan, Cricket A Malladi, Venkat S Dreszer, Timothy R Learned, Katrina Kirkup, Vanessa M Wong, Matthew C Maddren, Morgan Fang, Ruihua Heitner, Steven G ...

Published in Nucleic acids research

The Encyclopedia of DNA Elements (ENCODE), http://encodeproject.org, has completed its fifth year of scientific collaboration to create a comprehensive catalog of functional elements in the human genome, and its third year of investigations in the mouse genome. Since the last report in this journal, the ENCODE human data repertoire has grown by 898...

ENCODE whole-genome data in the UCSC genome browser (2011 update).

Raney, Brian J Cline, Melissa S Rosenbloom, Kate R Dreszer, Timothy R Learned, Katrina Barber, Galt P Meyer, Laurence R Sloan, Cricket A Malladi, Venkat S Roskin, Krishna M ...

Published in Nucleic acids research

The ENCODE project is an international consortium with a goal of cataloguing all the functional elements in the human genome. The ENCODE Data Coordination Center (DCC) at the University of California, Santa Cruz serves as the central repository for ENCODE data. In this role, the DCC offers a collection of high-throughput, genome-wide data generated...

The UCSC Genome Browser database: update 2010.

Rhead, Brooke Karolchik, Donna Kuhn, Robert M Hinrichs, Angie S Zweig, Ann S Fujita, Pauline A Diekhans, Mark Smith, Kayla E Rosenbloom, Kate R Raney, Brian J ...

Published in Nucleic acids research

The University of California, Santa Cruz (UCSC) Genome Browser website (http://genome.ucsc.edu/) provides a large database of publicly available sequence and annotation data along with an integrated tool set for examining and comparing the genomes of organisms, aligning sequence to genomes, and displaying and sharing users' own annotation data. As ...

Current status and new features of the Consensus Coding Sequence database.

Farrell, Catherine M O'Leary, Nuala A Harte, Rachel A Loveland, Jane E Wilming, Laurens G Wallin, Craig Diekhans, Mark Barrell, Daniel Searle, Stephen M J Aken, Bronwen ...

Published in Nucleic acids research

The Consensus Coding Sequence (CCDS) project (http://www.ncbi.nlm.nih.gov/CCDS/) is a collaborative effort to maintain a dataset of protein-coding regions that are identically annotated on the human and mouse reference genome assemblies by the National Center for Biotechnology Information (NCBI) and Ensembl genome annotation pipelines. Identical an...

The telomerase essential N-terminal domain promotes DNA synthesis by stabilizing short RNA-DNA hybrids.

Akiyama, Benjamin M Parks, Joseph W Stone, Michael D

Published in Nucleic acids research

Telomerase is an enzyme that adds repetitive DNA sequences to the ends of chromosomes and consists of two main subunits: the telomerase reverse transcriptase (TERT) protein and an associated telomerase RNA (TER). The telomerase essential N-terminal (TEN) domain is a conserved region of TERT proposed to mediate DNA substrate interactions. Here, we h...

GtRNAdb 2.0: an expanded database of transfer RNA genes identified in complete and draft genomes.

Chan, Patricia P Lowe, Todd M

Published in Nucleic acids research

Transfer RNAs represent the largest, most ubiquitous class of non-protein coding RNA genes found in all living organisms. The tRNAscan-SE search tool has become the de facto standard for annotating tRNA genes in genomes, and the Genomic tRNA Database (GtRNAdb) was created as a portal for interactive exploration of these gene predictions. Since its ...

Whole-transcriptome RNAseq analysis from minute amount of total RNA.

Tariq, Muhammad A Kim, Hyunsung J Jejelowo, Olufisayo Pourmand, Nader

Published in Nucleic acids research

RNA sequencing approaches to transcriptome analysis require a large amount of input total RNA to yield sufficient mRNA using either poly-A selection or depletion of rRNA. This feature makes it difficult to miniaturize transcriptome analysis for greater efficiency. To address this challenge, we devised and validated a simple procedure for the prepar...

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