Different Genome browser .....

Genome:

Genomics is a discipline in genetics that applies recombinan DNA technology, DNA

sequencing methods, and bioinformatics to sequence, assemble and analyze the function and structure of genomes, the complete set of DNA within a single cell of an organism.

The term “genomics” was coined by Dr. Tom Roderick, a geneticist at the Jackson

Laboratory.

Genomics study can be tentatively divided into structural genomics and functional

genomics.

Genome Browser:-

Genome browser provides a graphical interface for users to browse, search, retrieve and analyze genomic sequence and annotation data.

Web-based genome browsers:-

There are two types of web-based genome browsers. Web-based genome browsers can be classified into general genome browsers with multiple species and species-specific genome

browsers.

 The multiple-species genome browsers :-

the UCSC genome database, the Ensembl

project ,the NCBI Map viewer, the Phytozome and Gramene platforms.

 Species-specific genome browsers :- implemented based on the GBrowse framework,

 Such as MGI, FlyBase, WormBase, SGD and TAIR.

Ensembl:-

Ensembl genome database project is a joint scientific project between the European

Bioinformatics Institute and the Wellcome Trust Sanger Institute, which was launched in 1999 in

response to the imminent completion of the Human Genome Project. Ensembl aims to provide a centralized resource for geneticists, molecular biologists and other researchers studying

the genomes of our own species and other vertebrates and model organisms. Ensembl is one of several well known genome browsers for the retrieval of genomic information.

Ensembl is a genome browser for vertebrate genomes that supports research in

comparative genomics, evolution, sequence variation and transcriptional regulation. Ensembl annotate genes, computes multiple alignments, predicts regulatory function and collects disease data. Ensembl tools include BLAST, BLAT, BioMart and the Variant Effect Predictor (VEP) for all supported species.

Retrieving Data from Ensembl :-

A BioMart powered query system is provided for bulk data retrieval, and advanced users can

use standard Mart API to retrieve bulk data from the backend database directly. Furthermore,

sequence similarity searches with BLAST/BLAT and other tools such as assembly converter, ID

history converter, region report and variant effect predictor are supported for users to process

data conveniently.

UCSC:-

The UCSC Genome Browser is an on-line, and downloadable, genome browser hosted

by the University of California, Santa Cruz (UCSC). 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 is a graphical viewer optimized to support fast interactive performance and is an open-source, web-based tool

suite built on top of a MySQL database for rapid visualization, examination, and querying of the

data at many levels. The Genome Browser Database, browsing tools, downloadable data files,

and documentation can all be found on the UCSC Genome Bioinformatics website.

Analysis tools:-

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 FAST sequence alignment tool

BLAT[6] 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.

A liftOver tool uses whole-genome alignments to allow conversion of sequences from one

assembly to another or between species. The Genome Graphs tool allows users to view all

chromosomes at once and display the results of genome-wide association studies (GWAS). The

Gene Sorter displays genes grouped by parameters not linked to genome location, such as

expression pattern in tissues.

Genome Browser :- 

interactively visualize genomic data

BLAT:- rapidly align sequences to the genome

Table Browser :-download data from the Genome Browser database

Variant Annotation Integrator:- get functional effect predictions for variant calls

Data Integrator:- combine data sources from the Genome Browser database

Genome Browser in a Box (GBiB):- run the Genome Browser on your laptop or server

In-Silico PCR:- rapidly align PCR primer pairs to the genome

LiftOver:- convert genome coordinates between assemblies.