Genome Annotation by Although obtaining the DNA sequence of any organism is a significant technological feat, the sequence obtained is really not that useful without further information.
For an example, imagine Stephen King goes on vacation. 12 hours in, he gets an idea for a book...a reall whopper. Probably his masterpiece. The only thing he has to work with is a beat up underwriter manual typewriter and large pile of papers that have already been typed on one side.
As he starts typing, he notices that none of the punctuation on the typewriter works. Not even the space bar. But he's got to get the book onto paper, so he pounds away. 24 hours into his vacation, the story is complete: 1200 pages. With no punctuation and no indication of where a word, sentence, paragraph or chapter begin or end.
That's essentially what we are dealing with when we start with a sequences genome.
To make sense of the information, it has to be broken down into informational units like protein coding and non-coding regions. Transcribed regions, non-transcribed regions and regulatory elements. Protein binding domains, Long Terminal Repeat, Short Terminal Repeat, etc.
As the structure of the primary DNA sequence is elucidated, the sequence is annotated to indicate these informational elements. These elements can be (and are) grouped into separated "tracks" of information that can be overlayed on the original sequence. So you will find tracks containing information like protein coding sequences, mRNA and Expressed Sequence Tags.
This is where the genome viewer/browser comes in.
A genome browser provides an graphically organized way of selecting the annotation "tracks" you want to overlay on the primary DNA sequence of a genome. Given the amount of information available and with more available every day, it probably goes without saying that there can be a steep learning curve for using these tools. And there are peculiarities and advantages to most. One suggestion would be to start with one and stick with it until you discover another tool that you know will work better for you.
About the Ensemble Project:
The Ensemble project provides a host of online software tools for analysis of the annotated genomes of more than 70 organisms. Ongoing updates and revisions to annotation are based on a combination of evidence-based automatic and manual methods. The primary Ensemble genome collection focuses mainly on vertebrate organisms including human, mouse, xenopus, and zebra fish. However, the genomes of other model organisms such as C. elegans, fruit fly and S. cerevisiae are also available.
Ensemble Help and Documentation
Genomes of additional taxa are available from the related collections Ensemble Bacteria, Ensemble Fungi, Ensemble Metazoa, Ensemble Plants and Ensemble Protists.
Particularly Useful Tools:
BLAST/BLAT Genome Sequence Searching:
This implementation of the Basic Local Alignment Search Tool (BLAST) and BLAT, the related BLAST-Like Alignment Tool, allow you to perform alignments between sequences you provide and any of the available Ensemble genome sequence databases. BLAST allows you to search for related, but not identical sequences, whereas the faster BLAT allows you identify alignments between a nearly identical probe and genome sequences.
The NCBI Genome Data Viewer (GDV) is a genome browser supporting the exploration and analysis of annotated eukaryotic genome assemblies. The GDV browser can visualize different types of molecular data in a whole genome context, including gene annotation, BLAST alignments, and experimental study data from the NCBI GEO and dbGaP databases. GDV release notes describe new features relating to this browser.
References:
Flicek P, Fitzgerald S, Gil L, Girón CG, Gordon L, Hourlier T, Hunt S, Johnson N, Juettemann T, Kähäri AK et al. 2014. Ensembl 2014. Nucleic Acids Research 42(1):D749-D755.
Abecasis GR, Altshuler D, Auton A, Brooks LD, Durbin RM, Gibbs RA, Hurles ME, McVean GA, Genomes Project C. 2010. A map of human genome variation from population-scale sequencing. Nature 467(7319):1061-1073.
Abecasis GR, Auton A, Brooks LD, DePristo MA, Durbin RM, Handsaker RE, Kang HM, Marth GT, McVean GA, Genomes Project C. 2012. An integrated map of genetic variation from 1,092 human genomes. Nature 491(7422):56-65.
About the UCSC Genome Browser:
The UCSC Genome Browser is a free web tool that allows you visualize and compare annotation "tracks" along a desired genomic sequence. Quick access over 90 complete genomes viewable from the UCSC Genome Browser is provided through the UCSC Genome Bioinformatics website.
UCSC Genome Bioinformatics Website
UCSC Genome Browser Help and Documentation:
Guide to the UCSC Genome Browser
This is a a very good web based tutorial that shows you how to use the UCSC Genome Browser to find a protein-coding gene and the available annotations for that gene. The tutorial is a great starting point given it's tight focus on providing specific examples of basic concepts underlying the browser.
This is a journal article that provides practical information about using the genome browser AND the associated tools BLAT, Custom tracks, Table Browser, Sessions and In silico PCR. Unlike the "Guide to the UCSC GEnome Browser, this tutorial provides an overview of many of the resources available from the UCSC Bioinformatics website. Not sure what BLAT, Custom tracks, Table Browser, Sessions and In silico PCR are or whether they might be useful? This tutorial is a great place to start.
Genomes from over 300 Bacteria and Archaea species can be viewed from the UCSC Microbial Genome Browser.
Particularly Useful Tools:
Select a genome, enter a pair of PCR primer sequences and discover the sequence(s) of the most likely PCR products from a reaction containing your selected template/primer set.
Graphically display available genome-wide data sets along an entire genome. Use this active display to quickly navigate to that region in the UCSC browser. The help page for Genome Graphs is here.
References:
Harte, R. A., Diekhans, M., Kent, W. J. & Haussler, D. Guide to the UCSC Genome Browser. Cambridge, MA: NPG Education, 2010.
Zweig AS, Karolchik D, Kuhn RM, Haussler D, Kent WJ. 2008. UCSC genome browser tutorial. Genomics 92(2):75-84.
About the NCBI Map Viewer:
NCBI Map Viewer provides basic visualization capabilities for a large subset of the genome sequences available through the NCBI site. While the other two genome browsers provided on this subject guide (i.e. Ensemble and UCSC Genome Viewer) are under active development, Map Viewer has remained fairly stable over the last half decade or so. However, NCBI Map Viewer has the notable advantages of a much shallower learning curve and being well and deeply integrated into the NCBI site structure.
Particularly Useful Tools:
Not a single tool, per se, this page serves as a gateway to several other genome-related tools at the NCBI site. In particular, BLAST the Human Genome and Genome Decoration Page are useful.