After a rough start, this form will now accomodate non-fasta formatted input including Microsoft Word files. In some browsers, if your input file has a ".doc" file extension, the output files created by this form will download to your disk instead of displaying as a web page (?).
This form takes an input DNA sequence file in fasta format, derives all di-, tri-, and tetra- nucleotide repeats in the sequence, masks the sequence around the repeats for larger repetitive sequences, and then designs unique primer pairs to amplify the simple sequence repeats. These are potentially polymorphic simple sequence repeats (SSRs) that can be used in genetic mapping/positional cloning projects.
Credits:This site uses software including repeatmasker, primer3 (Whitehead Institute), and components of the Emboss programs. Zebrafish repeat libraries compiled by Rick Waterman and Zhirong Bao. Human and mouse repeat libraries are from the Genetic Information Research Institute. Thanks to Gary Williams for fine tuning the eprimer3 program that makes primer selection possible.
Created
and maintained by Iain
Drummond,
Renal Unit, Massachusetts
General Hospital
Last updated 2/19/2005
