[Bioinformatics] Science Functional Genomics Resources: Genome Maps

Win Hide winhide@sanbi.ac.za
Tue, 09 Jan 2001 12:41:50 +0200 

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    Science Functional Genomics Resources: Genome Maps
  

  

    

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Some Great Genome Viewers


	  

	    

	      
	      
	      
	    

	  

	  
          

            

              
	      

	      
	      
	      
 

	      
Introduction

	      
Genomes have gotten a lot of attention lately.  Large-scale seq=
uencing methods and powerful computers have finally allowed the sequence =
of the human genome to be essentially completed.  This milestone, though,=
 has not been achieved in a vacuum:  many other experimental systems have=
 been fully sequenced for months or even years.  Although each of these g=
enomes are interesting and valuable in their own right, the collection of=
 sequenced genomes is more valuable still.  The quantity of data allows r=
esearchers to finally start making meaningful comparisons across genomes.=
  Easy genome access, analysis, and comparison creates an environment in =
which unknown genes can be understood based on their similarity to other =
genes, and inter- and intra-genome sequence trends can be detected and ap=
preciated.


	      
Essential to this effort are computers and the software that dr=
ives the genomics effort.  In order to make sense of the billions of sequ=
enced bases, many research groups have developed their own viewers to let=
 them visualize their own data; in the spirit of cooperation, many of the=
se tools have been freely released to the public.  Commercial interests h=
ave also started to release their own tools, some drawing on proprietary =
databases.   The scope, power, and ease-of-use of these genome viewers va=
ries considerably.  Here we present a sampling of some of the more impres=
sive options for viewing genomic data.


	      
In selecting this initial set of viewers, we looked for softwar=
e that allowed users to navigate the genome by either searching for a fea=
ture directly, or browsing the genome as a whole.  We also selected sites=
 that offered graphical interfaces and were accessed through the Internet=
, both to simplify getting started and to ensure that data were up-to-dat=
e.  All viewers require an Internet connection (dedicated, high-speed is =
preferred, especially for long downloads); a fast processor, plenty of me=
mory, and a large color monitor also make using these sites much more pro=
ductive.



Jeff Plautz

HighWire Press



	      
	      



	      

	      

	      Site name: Saccharomyces Genome Dat=
abase

	      Institution: Department of Genetics, Stanford University Sc=
hool of Medicine

	      Organism: S. cerevisiae

	      System requirements: Internet connection and Web browser
	      

	      

	      A very nice viewer for yeast genome data.  Several map types are a=
vailable (genomic and a correlated physical/genetic map).  Searching was =
straightforward, and graphical browsing was very intuitive.  Response tim=
e across the site was quite fast, and there were ample links to follow fo=
r additional information; however, some of the links for related informat=
ion (literature, for example) did not have any meaningful information beh=
ind them.  The site also contained a number of other sequence analysis to=
ols for yeast research.
	      

	      

	      


	      
	      


	      

	      

	      Site name: NCBI Map Viewer

	      Institution: National Center for Biotechnology Information<=
br>
	      Organisms: Homo sapiens, Mus musculus

	      System requirements:  Internet connection and Web browser
	      

	      

	      This viewer is brought to us from the NCBI -- the people who devel=
oped PubMed and GenBank.  Data is linked extensively between the viewer a=
nd the other NCBI data sources, although it's easy to get lost in the nav=
igation across resources, especially if your browsing takes you to a diff=
erent gene or region.  Vertical display of data somewhat limits the graph=
ical field compared to other horizontal-oriented tools, so a large monito=
r is especially helpful here.  Chromosome summary information and a full-=
chromosome orientation map that always appears on the screen are a few of=
 the features that make using the graphical interface a simple experience=
=2E
	      

	      


	      


	      
	      


	      

	      

	      Site name: Draft Human Genome Browser

	      Institution: University of California, Santa Cruz (Jim Kent=
)

	      Organism: Homo sapiens

	      System Requirements: Internet connection and Web browser
	      

	      

	      This human genome viewer offers the most different types of inform=
ation diplayable on the screen at one time.  Features range from predicte=
d genes to ESTs to GC content, to name a few.  There are many options for=
 display, making the type of information as well as the window size almos=
t completely under user control.  Response time across the site is fast, =
although searches do tend to return a number of false positive results (o=
ften in addition to the desired result) due to the one-box-fits-all searc=
h strategy. Information beyond the viewer's display is limited to preform=
ed searches against some NCBI databases.
	      

	      
 =



	      


	      
	      



	      

	      

	      Site name: The=
 Genome Channel

	      Institution: Oak Ridge National Laboratory Computational Bi=
osciences Section

	      Organisms: Many (> 25)

	      System Requirements: Internet connection and Java-capable W=
eb browser
	      

	      

	      The Genome Channel offers more genomes in a standard viewer format=
 than any other site we've seen.  This makes comparisons between multiple=
 genomes side-by-side (-by-side-by-side...) possible. The tool runs throu=
gh a Java applet, which is generally slower than non-applet sites and can=
 cause some problems with many common platform/browser configurations.  T=
hese problems can often (but not always) be solved with some software upg=
rades, and the resulting product is impressive.  Although the user interf=
ace isn't quite as simple as some other viewers, it works well with pract=
ice.
	      

	      
 =



	      


	      
	      



	      

	      

	      Site name: GeneSeen

	      Institution: Berkeley Drosophila Genome Project

	      Organism: Drosophila melanogaster

	      System requirements: Internet connection and Java-capable W=
eb browser
	      

	      

	      This viewer runs through a Java applet, so it's not flawless acros=
s machines -- Mac and Linux users may experience some problems, and Windo=
ws users may also need to upgrade their software to get the viewer to wor=
k.  This viewer is worth it, though.  Navigation is smooth, and there is =
a nice correlation between the feature diagram and the cytological map of=
 the chromosome.  The large amount of genetic information can take a whil=
e to load, which can be frustrating for a user (especially on a slow conn=
ection) who is interested in a large stretch of the genome.  Still, navig=
ation is very straightforward and informative.
	      

	      



	      
	      


	      
	      

	      		
            

          

	  
Questions?  Comments?  Let us=
 know.

	  
 

	  

        		
      

    

    

    

      

        

         

          Copyright &co=
py; 2000 by The American Association for the Advancement of Science.

         

         		
      


      

        
      

    

    
  


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