Title: GeneCards , LocusLink and NiceProt View from SWISSPROT
NiceProt View from SWISSPROT:http://ca.expasy.org/sprot/
Date Reviewed: May 21, 2001
Reviews on GeneCards, Locuslink and NiceProt
Thanks to the rapid development of bioinformatics,today's online bioinformatics database provide almost everything you can know about a gene or a protein. It is just a question how you find it. Here I compare three major gene or protein review sites online: GeneCards from Weizmann Institue of Science,ISRAEL;LoucsLink from NCBI and Niceprot View in SWISSPROT from SIB(Swiss Institute of Bioinformatics).
GeneCards is possibly the oldest one among these three.However,the interface hasn't change much in the past three years, possible due to their funding problem. They obviously don't have as much money as NCBI or SIB.Recently, DoubleTwist signed an aggreement with Weizmann Institute to commercialize the Weizmann Institute's GeneCards™ database and fund further for the development of GeneCards.
GeneCards is exclusively reviews on human genes. It clarms to contain more than 20,000 human genes which is about two third of total human genes.The nice thing about this site is that it puts all the gene relative sites together. Its search engine is just Ok. For example, when I search for CD22,unlike SWISSPROT or Loucslink, which only returned two hits: mouse CD22 and human CD22, GeneCards gave me 6 hits. Considering GeneCards is only a human gene database, this is not good. The big problem about GeneCards is that it doesn't have much their own stuff. Meanwhile it faces strong competetion from locuslink of NCBI.
The Locuslink in NCBI is usually my first stop when I want to find something about a gene. Under the strong support from NCBI, Locuslink is now getting better and better. Locuslink provides extensive information on human,mouse, rat, fly,and Danio rerio genes.It now has nearly 20,000 human gene records and 31,000 mouse gene records.
Its search engine is good. Due to the different name for the same gene and the same name for the different gene,it may return multiple results. It is better to turn the display option to "summary" instead of "brief" when you do the search sothat you can determine which hit is you really want.
Locuslink has a good cross-link inside NCBI. From locuslink, you can get mRNA,DNA as well as protein sequence precisely from the links under it.It also provides link to OMIM,PROW,SNP,GDB and GeneCards if they are available. However, Locuslink doesn't have very good information on proteins, expecially protein domain, secondary structure and 3D structure. SWISSPROT does a good job on these things.
NiceProt View from SWISSPROT is a very good site on protein review.Its feature table has good protein annotations on glycosalation sites, disuflate bonds and transmembrane domains. Best of all,it provides protein domain prediction result directly from Interpro,Block,Pfam,SMART and ProDom. Basically, it is a protein review site. It does nothing on DNA.
In summary, Locuslink has very extensive information relative to a gene. NiceProt view form SWISSPROT does better on protein. As for the GeneCards, you can access it from locuslink.I won't set it as my start point. One last thing, you can reach Locuslink and NiceProt from NCBI and EXPASY very easily. For GeneCards, I just can't remember its URL.
Evaluation: GeneCards: *
NiceProt View: ***
Reviewer: Lei jin