A Dummy's Guide to Genbank

A Dummy's Guide to Genbank


There is a wealth of genetic information available at Genbank at http://www.ncbi.nlm.nih.gov/ about the genomes of humans and other organisms, but it can be difficult to access for non-experts. I hope that this brief guide will assist others to learn their way around this site faster than I did.

When you get to Genbank, I would recommend clicking on the Human-Mouse Homology Maps. Here you will see numbers representing the 23 human and 20 mouse chromosomes. You can explore them by clicking on them; suppose you click on human chromosome 11 . You will see a list of genes and the corresponding mouse genes. On the very left you will see something called RH Map. To me this is the most interesting part. Let's say we click on the RH map for gene IGF2, which is labeled WI-14149, in the left column. You will then see a table of the similarities of a human protein to that from several different organisms. The protein is called the "PUTATIVE INSULIN-LIKE GROWTH FACTOR II ASSOCIATED PROTEIN," and you will learn that it is

100 % similar to a Homo Sapiens protein
81 % similar to a Mus musculus (mouse) protein
81 % similar to a Rattus norvegicus (rat) protein
90 % similar to a Bos taurus (cattle) protein
76 % similar to a Sus scrofa (pig) protein

If you don't know the technical name of a listed organism, you can click on the link to the left, and it will give the common name, as well as a lot of other information about the gene. If you click on a mouse chromosome, you can obtain the same kind of information, but the RH Map will be further over to the right. I wish that there were more information about the similarity between human and ape proteins, but it seems to be very scarce, for whatever reason. But there are a few entries. The name for chimpanzees in the database is Pan troglodytes, by the way. The name for gorilla is just Gorilla gorilla.

You can also go to the The NCBI Taxonomy Homepage, where you can click on the tree link to find information about the various organisms whose genes are stored in the database. In fact, you can search for information under the common name of the organism (such as "pig").

I hope you find this material interesting, but you may be surprised at how similar we are to the pig!

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