1. Use Genbank to obtain a series of proteins of interest from at least four different species.
Genbank
http://www.ncbi.nlm.nih.gov/

Genbank output looks like this:

Pick PROTEIN or complete cDNA sequences from 4 or five different species, should include a range of vertebrate (and invertebrate) species one at a time. Gene sequences may have introns so are not useful.  Thiis the output for a complete cDNA sequence.

Paste accession number, organism and protein sequence into a word file.  Typically the protein translation appears with the nucleotide sequence if a nucleotide sequence is what you have.  If not we can translate with the computer.

Each sequence should have a FastA format header, as for example :

>BE191962 Xenopus C reactive protein

Save your word document by posting a copy into a folder in our shared files.

Paste all the text from the word document into Blockmaker

Blockmaker finds conserved regions

http://blocks.fhcrc.org/blockmkr/make_blocks.html

 
Print out the blockmaker results for later use. SAVE an electronic copy by posting it to a folder in our shared files.

Use the link in blockmaker to send the blocks directly to

CODEHOP
http://blocks.fhcrc.org/blocks/codehop.html

Print out the results from CODEHOP. This program chooses primer pairs with matched annealing temperatures for PCR

So far I don't know how to save the results in a legible format, but do save the output as a web page into that folder in our shared files.

Then we consult about ordering primers

Good luck!