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The UCSC genome browser and associated tools.

The UCSC Genome Browser (http://genome.ucsc.edu) is a graphical viewer for genomic data now in its 13th year. Since the early days of the Human Genome Project, it has presented an integrated view of genomic data of many kinds. Now home to assemblies for 58 organisms, the Browser presents visualization of annotations mapped to genomic coordinates. The ability to juxtapose annotations of many types facilitates inquiry-driven data mining. Gene predictions, mRNA alignments, epigenomic data from the ENCODE project, conservation scores from vertebrate whole-genome alignments and variation data may be viewed at any scale from a single base to an entire chromosome. The Browser also includes many other widely used tools, including BLAT, which is useful for alignments from high-throughput sequencing experiments. Private data uploaded as Custom Tracks and Data Hubs in many formats may be displayed alongside the rich compendium of precomputed data in the UCSC database. The Table Browser is a full-featured graphical interface, which allows querying, filtering and intersection of data tables. The Saved Session feature allows users to store and share customized views, enhancing the utility of the system for organizing multiple trains of thought. Binary Alignment/Map (BAM), Variant Call Format and the Personal Genome Single Nucleotide Polymorphisms (SNPs) data formats are useful for visualizing a large sequencing experiment (whole-genome or whole-exome), where the differences between the data set and the reference assembly may be displayed graphically. Support for high-throughput sequencing extends to compact, indexed data formats, such as BAM, bigBed and bigWig, allowing rapid visualization of large datasets from RNA-seq and ChIP-seq experiments via local hosting.

Pubmed ID: 22908213 RIS Download

Mesh terms: Animals | Computational Biology | Computer Graphics | Data Display | Data Mining | Databases, Genetic | Genomics | Humans | Information Storage and Retrieval | Internet | Search Engine | Sequence Alignment | Software

Research resources used in this publication

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Data used in this publication

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Associated grants

  • Agency: NHGRI NIH HHS, Id: P01HG5062
  • Agency: NICHD NIH HHS, Id: RC2HD064525
  • Agency: NHGRI NIH HHS, Id: U41HG004568
  • Agency: NIEHS NIH HHS, Id: U01ES017154
  • Agency: NHGRI NIH HHS, Id: U01HG004695
  • Agency: NHGRI NIH HHS, Id: U41HG004269
  • Agency: Howard Hughes Medical Institute, Id: P41HG002371
  • Agency: NHGRI NIH HHS, Id: U01DE20057
  • Agency: NIDCR NIH HHS, Id:

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This is a list of tools and resources that we have found mentioned in this publication.


UCSC Genome Browser

A collection of genomes which include reference sequences and working draft assemblies, as well as a variety of tools to explore these sequences. The Genome Browser zooms and scrolls over chromosomes, showing the work of annotators worldwide. The Gene Sorter shows expression, homology and other information on groups of genes that can be related in many ways. Blat quickly maps your sequence to the genome. The Table Browser provides access to the underlying database. VisiGene lets you browse through a large collection of in situ mouse and frog images to examine expression patterns. Genome Graphs allows you to upload and display genome-wide data sets. Also provided is a portal to the Encyclopedia of DNA Elements (ENCODE) and Neandertal projects.

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