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The UCSC site hosts a set of genome analysis tools, including a full-featured GUI interface for mining the information in the browser database, a FASTA format sequence alignment tool BLAT [9] that is also useful for simply finding sequences in the massive sequence (human genome = 3.23 billion bases [Gb]) of any of the featured genomes.
UC Santa Cruz posted the first human genome sequence on the internet on July 7, 2000, to make it freely available to the public. [2] Kent then immediately began to assemble the UCSC Genome Browser to allow researchers to view the assembled DNA sequence in terms of genes and chromosomes. [3]
The UCSC browser limits query sequences to less than 25,000 letters (i.e. nucleotides) for DNA searches and less than 10,000 letters (i.e. amino acids) for protein and translated sequence searches. [8] Figure 2: Using web-based BLAT to search a target database with a DNA query sequence. The search parameters can be seen above the query sequence ...
The CCDS project tracks identical protein annotations on the reference mouse and human genomes with a stable identifier (CCDS ID), and ensures that they are consistently represented by the National Center for Biotechnology Information , Ensembl, and UCSC Genome Browser. [1]
MethBase: database of DNA methylation data visualized on the UCSC Genome Browser; Minimotif Miner: database of short contiguous functional peptide motifs; Oncogenomic databases: a compilation of databases that serve for cancer research; PubMed: references and abstracts on life sciences and biomedical topics; RIKEN integrated database of mammals
DECIPHER is a web-based resource and database of ... InDels), from over 25000 patients and maps them to the human genome using Ensembl or UCSC Genome Browser. ...
A track hub is a structured directory of genomic data, such as gene expression or epigenetic data, viewable over the web with a genome browser. Track hubs are defined by the track hub standard. [1] Originally developed as part of the UCSC genome browser, they are now supported by Ensembl and BioDalliance. [2]
The pilot stage of ENCODE, involving development of a web browser to show experimental results related to regions on the human genome sequence, was undertaken at UCSC. [3] The university team maintain and develop the UCSC Genome Browser to provide the public with access to genome data from an increasing number of animals, mainly vertebrates ...