genome browsers allow researchers to navigate the genome in an analogous way to navigating the internet with internet explorer or mozilla . as with the internet
, the amount of available genomic data is overwhelming , and browsers aim to make these data accessible to all researchers .
the number and variety of annotations has increased dramatically , enabling a detailed view of many aspects of the genome .
of course , one of the primary annotations is still the location and structure of genes , but even this is not straightforward , as many sources of information ( sometimes confiicting ) necessitate the creation of several gene - related annotations .
these include the locations of mrna and expressed sequence tag ( est ) sequences deposited in the major sequence databases , curated gene sequence projects such as the vertebrate genome annotation ( vega ) , ref seq , mgc   and ensembl   and computational predictions such as genscan   and twinscan .
the locations of clones from bacterial artificial chromosome ( bac ) and other clone libraries , sequence - tagged site ( sts ) markers from genetic maps [ 7 - 9 ] and estimated boundaries of cytogenetic bands   provide crucial mapping information .
alignments with genomic sequences from other species delineate regions of synteny and help to identify orthologous genes .
single nucleotide polymorphisms ( snps ) and other types of variation point to differences within a species .
locations of repetitive sequences , due both to retrotransposable elements and to simple repeats such as microsatellites , help to provide a more complete description of the genomic landscape .
browsers simultaneously display these annotations , allowing for the investigation and appreciation of the genomic context in which to consider a gene or region of interest . a sample of annotations found in one or more of the ucsc , ensembl and ncbi genome browsers .
abbreviations : bac , bacterial artificial chromosome ; est , expressed sequence tag ; gnf , genomics institute of the novartis research foundation ; ncbi , national center for biotechnology information ; rh , radiation hybrid ; snp , single nucleotide polymorphism ; sts , sequence - tagged site ; ucsc , university of california santa cruz ; vega , vertebrate genome annotation . three browsers in particular , the university of california santa cruz ( ucsc ) genome browser ( http://genome.ucsc .
edu ) , the ensembl genome browser ( http://www.ensembl.org ) and the national center for biotechnology information ( ncbi ) mapviewer ( http://www.ncbi.nih.gov/mapview ) provide information portals for multiple genome sequences , including human .
genome browsers can be described and compared with respect to presentation , content and functionality .
presentation refers to how the data are displayed in a graphical form and the overall structure of the website .
content refers to what data is accessible , such as particular genome sequences and annotations for a specific genome .
functionality refers to tools available for mining the genome sequence and annotations , such as sequence and text searches and data extraction .
the ucsc , ensembl and ncbi genome browsers aim to present genomic data in a manner that will facilitate research , but they do so in different ways . table 2 summarises some of these differences , and a more complete , yet still high - level , discussion of these is presented below .
abbreviations : blat , blast - like alignment tool ; encode , encyclopedia of dna elements ; e - pcr , electronic polymerase chain reaction ; ncbi , national center for biotechnology information ; ssaha , sequence search and alignment by hashing algorithm ; ucsc , university of california santa cruz ; vega , vertebrate genome annotation .
ucsc features three types of browsers : a genome browser , a gene family browser ( gene sorter ) and a proteome browser .
the genome browser is the most widely used and will be the focus of this discussion , although this in no way implies that the other two are not very valuable research tools .
the primary web page of the genome browser consists of a graphic that displays annotations for some specified genomic region surrounded by navigational buttons and links to tools .
the navigational buttons allow for zooming in and out or moving left or right along the genomic sequence . within the graphic , annotations -- also referred to as ' tracks ' -- are displayed horizontally , with the genome sequence running from left to right .
the locations of specific elements within annotations are primarily indicated by boxes with lines sometimes connecting them to show relationships , such as in gene structures ( boxes = exons , lines = introns ) .
the use of different colours and shading of boxes highlights the properties of certain annotations , such as confidence in the underlying data -- as is the case in the known genes track -- and quantitative traits , employed by the gc percent track to indicate differing levels of content of guanine ( g ) and cytosine ( c ) base pairs . clicking on an element within an annotation
will bring up a separate ' details ' web page with specific information about that element and links to other databases and resources such as genbank   and swissprot .
drop - down menus towards the bottom of the page , also accessible through a separate ' configuration ' page , allow for the selection of annotations to display in the graphic ( table 1 ) .
, there are 22 views that display different types of data and/or provide various functions .
the primary view , analogous to the ucsc main browser page , is the contigview . within this view
are three graphic displays that provide information at different resolutions for a region in the genome .
the overview graphic displays multiple megabases ( mbs ) , the detailed view shows approximately 1 mb and the basepair view details about 100 bases .
similarly to ucsc , the genome is shown in a horizontal fashion with navigational buttons located within the detailed view graphic . in the three graphics on this page ,
annotations are delineated by boxes , sometimes connected by lines and other times contained within a larger box . in the detailed and basepair views ,
the dna contigs annotation divides the graphic with elements on the forward strand appearing above and on the reverse strand below .
clicking on an element in an annotation will cause a small pop - up window to appear with some basic information and possibly links to other views within ensembl or resources at other sites .
for example , clicking on an ensembl gene provides links to geneview , transcriptview and protview pages , which contain additional information about the gene or a region of the gene .
menus at the top of the detailed view graphic provide the ability to select specific annotations for display .
the primary display of ncbi 's mapviewer differs significantly from both ucsc and ensembl by orienting the genome sequence in a vertical fashion .
again , boxes and lines indicate positions of elements in annotations , also referred to as ' maps ' , which are presented in columns . the ability to navigate the genome
links within the annotations , as well as the linkout column , provide easy access to other relevant resources at the ncbi , such as entrez gene ( formerly locuslink ) , online mendelian inheritance in man ( omim ) and dbsnp .
a ' maps & options ' button brings up a separate window , allowing one to select annotations to display .
the ncbi provides access to the largest number of genome sequence assemblies , including 11 vertebrates , five invertebrates , one protozoan , eight plants and 12 fungi .
ensembl and ucsc are more heavily slanted towards the larger eucharyotic genomes , providing access to a similar set of 13 vertebrate genomes and six ( ensembl ) or 15 ( ucsc ) invertebrates , and are devoid of the other classes of species .
annotations available within the ncbi mapviewer primarily originate in the numerous databases available at the ncbi .
the mapviewer , therefore , is very tightly integrated with these data sources , some of which -- such as the mitel - man breakpoint annotation -- are not available at the other sites .
ucsc and ensembl also present annotations that originate from outside resources , such as the databases at ncbi , but supplement these with numerous additional annotations contributed by in - house or third - party researches .
the ucsc browser arguably contains the broadest set of annotations , especially in the area of cross - species comparions .
for example , the conservation annotation , developed at and displayed only at ucsc , shows a measure of evolutionary conservation across eight vertebrate species , as determined by a phylogenetic hidden markov model .
ucsc is also the official repository for , and displays data from , the encode ( encyclopedia of dna elements ) project , containing annotations ranging from histone modifications to regions of dnase 1 hypersensitivity .
the ensembl browser contains the most extensive set of gene and transcription - related data , with 14 of its 22 views primarily focused on the presentation of gene- or protein - related data .
there is tight integration with gene data originating from both the ensembl genes annotation   -- a computationally generated evidence - based set that ensembl produces -- and the vega project   -- a manual curation effort .
the ensembl browser also has the most extensive presentation of haplotype data , especially in their ldview , which was generated by the hapmap project .
the underlying genomic sequence is exactly the same at all three sites , but analogous annotations may differ .
for example , locations of mrna and est sequences require an alignment to the genome sequence
. their precise alignment may vary , based on the alignment program used and specific parameter settings within the program .
the three sites do not employ the same alignment methods , resulting in slight differences , although they are in agreement for the vast majority of the time .
there are many common functions that all three sites provide . specific regions of interest can be quickly and easily displayed using keywords such as gene or marker names , exact base pair positions within chromosomes , or sequences via alignment programs like blast   ( ensembl and ncbi ) or blast - like alignment tool ( blat ) ( ucsc ) .
locations of paired primer sequences can be obtained via electronic polymerase chain reaction ( epcr ) ( ncbi and ensembl ) or ispcr ( ucsc ) .
ncbi allows users to view annotations in a tabular format that can then be downloaded into a text file .
ensembl 's biomart   and the ucsc table browser   allow for both simple downloads of annotations and for quite complex datasets to be generated . these two tools also allow for the uploading of files of genomic regions or names of genes or markers for which annotation data , including the underlying sequence , can be obtained .
ucsc and ensembl provide the ability for researchers to display their own annotation information within the browser .
a simple text file denoting the base pair locations of annotation elements is uploaded and used to create a corresponding temporary annotation within the graphic , which is essentially only viewable by the originator . in this way , researchers can usefully view their own data within the context of all other available genomic data .
ensembl provides the ability to view syntenic regions of two genomes simultaneously in their multicontigview .
the layout is similar to the contigview described previously , but with the addition of data from two separate genomes being displayed in the detailed view graphic , and a navigational view replacing the overview with a zoomed - out display of the regions being analysed in both genomes .
this overview of the ucsc , ensembl and ncbi genome browsers is by no means complete and is not meant to recommend the use of one or the other of these sites .
users should explore the capabilities of each browser to determine the one they prefer . in the end , the browser that allows a researcher to be the most productive is the best .
the genome browsers reviewed here provide access to not only human genome sequence data , but also to annotations from an ever - growing set of species .
similar functionality for each genome assembly is provided for all species , although the range of annotations varies dramatically . these are by no means the only genome - related browsers available , but they are among the most comprehensive .
similar browsers with more narrow foci , such as for a single organism , share many of the features and functions described above .
appropriate experimentation is required as necessary to test the accuracy of any hypothesis generated using these data .
nevertheless , genome browsers offer a powerful research tool to be utilised by researchers worldwide .
 the sequence of the human genome provides a scaffold on which numerous annotations , such the locations of genes , can be laid . 
 genome browsers have been created to allow the simultaneous display of multiple annotations within a graphical interface . 
 in addition , they provide the ability to search for markers and sequences , to extract annotations for specific regions or for the whole genome and to act as a central starting point for genomic research . 
 this review describes the basic functionality of genome browsers and compares three of them : the university of california santa cruz ( ucsc ) genome browser , the ensembl genome browser and the ncbi mapviewer . 
Introduction
Genome browser comparisons
Presentation
Content
Functionality
Last words