Friday, September 09, 2005

Molecular resources for monarch biology

One of the best places to get both sequence information and information on current research is the National Center for Biotechnology Information. The NCBI is part of the National Library of Medicine in the National Institutes of Health. One of the best known aspects of the NCBI is that they house GenBank, a collection of all the DNA and protein sequences that are publicly available. They also have PubMed, a database of scientific literature that's related to medical research.

To get sequence information for Monarch butterflies:

1. Go to the Taxonomy Browser at the NCBI

2. Search with the scientific name for monarchs: Danaus plexippus

This takes you to a page with the heading "Danaus plexiplus" and two subspecies. Click the Danaus plexippus link at the top of the list to get the taxonomy record.

There is a handy box in the upper right hand corner of the taxonomy record with useful links.

The links that are shown depend on the types of resources that are present in the NCBI databases. For monarch butterflies these links to records in the Nucleotide, Protein, Popset, PubMed Central, and Taxonomy databases. The numbers in the columns reflect the number of records. So, the nucleotide database has 52 sequences from monarch butterflies (as of this morning). The protein database has 72 total, for both of the subspecies.

You can also get the sequences straight from GenBank.

The other very handy links are Popset and PubMed Central. The PopSet reference for Danaus, is linked to a list of 12 different sets of sequences from population and evolutionary studies of butterflies. PopSet is a database with sets of sequences from evolutionary studies. If you look at the papers that are referenced in PopSet, they should include in the sequences for the primers that were used in the studies. The PopSet sequences are also great for making phylogenetic trees, but that subject will be a future post.

The PubMed Central link gives a list of several scientific literature citations for monarch butterflies. The cool thing about PubMed Central is that you can actually get the full text and read the entire paper, if you're so inclined. Scientific publishers are still experimenting with free, on-line access, so these may only be available for a limited time.

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