UCSC

BioCodeKb - Bioinformatics Knowledgebase

The Genome Browser at the University of California Santa Cruz provides a uniform graphical interface to sequences, features, and annotations of genomes across a wide spectrum of organisms, from yeast to humans. In particular, it covers seven nematode genomes. We can use the provided tools and visual aides to facilitate sequence feature detection and examination here. It helps the researchers to use their expertise to interpret data themselves by using UCSC which provides high quality genome annotation.


It is an interactive website offering access to genome sequence data from a variety of vertebrate and invertebrate species and major model organisms, integrated with a large collection of aligned annotations. The Browser presents visualization of annotations mapped to genomic coordinates.


Showing the data in the graphical format allows the browser to present link access to detailed information about any of the annotations. The gene details page of the UCSC Genes track provides a large number of links to more specific information about the gene at many other data resources, such as Online Mendelian Inheritance in Man (OMIM) and SwissProt etc.


There are three basic ways to specify a region to browse:

  1. By a range of chromosomal numerical positions

  2. By a gene name

  3. By an accession number


More flexibly, instead of exact positions, one can also search for a descriptive term (such as “kinase inhibitor”) that is present in gene records.


Once a region is selected, the Genome Browser can display a wide selection of sequences and features as tracks. The tracks are easily customizable.


One important extension of the Genome Browser is the ability to add custom tracks. Custom tracks allow users to incorporate their own or third party data into the browser so that imported sequence annotations can be inspected in the context of existing ones. Some tracks are here set in list;

  • Mapping and Sequencing

  • Genes and Gene Predictions

  • Phenotype and Literature

  • mRNA and EST

  • Expression

  • Regulation

  • Comparative Genomics

  • Variation data

  • Repeats


Tools in UCSC

  • Genome Browser

  • BLAT

  • Table Browser

  • Variant Annotation Integrator

  • Data Integrator

  • Genome Browser in a Box (GBiB)

  • In-Silico PCR

  • LiftOver

  • Track Hubs

  • REST API


The Table Browser is a full-featured graphical interface, which helps us in querying, filtering and intersection of data tables. The Saved Session feature allows users to store and share customized views, increasing 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.


Uses

  • For viewing the genomic annotations.

  • Analysis of genome assembly

  • To allow viewing of data at any scale, from single basepair resolution to a whole chromosome

  • Display different kinds of conservation of data

  • Get genome, chromosomes and gene sequences

  • Find gene density

  • Study about the positions of SNP

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