Find new candidate SSR markers/primer pairs in the Sanger Center Zv8 assembly of the zebrafish genome, or in BAC sequence.
updated with Zv8 and Sanger finished and unfinished bacs 5-10-2009

Zebrafish
BLAST

Please note: search format change (3/07): Due to a change in how bac sequence is available from the Sanger Center, use bac names (i.e. zK146H10) for searches instead of accession numbers. BAC accession numbers (i.e. BX465862.7) are no longer accepted as input.

Enter the name of a Zv8 scaffold, or BAC name. Sanger BAC name formats:

Searches take between 1 and 3 minutes to complete. Input is case sensitive and won't accept blank spaces.

This form no longer searches for Zv3, Zv4, Zv5, Zv6 or Zv7 contigs.

This form searches for a Zv8 scaffold, finished or unfinished BAC clone by name, derives all di-, tri-, and tetra- nucleotide repeats in the sequence, masks the sequence around the repeats for larger zebrafish 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.

Note: Due to the possibility of mis-assembly in zebrafish genome assemblies, marker linkage should be independently confirmed.

Credits:This site uses the Sanger Center zebrafish Zv8 assembly, and bac sequence, and software including repeatmasker, primer3 (Whitehead Institute), and components of the Emboss programs. Zebrafish repeat libraries compiled by Rick Waterman and Zhirong Bao. Thanks to Gary Williams for fine tuning the eprimer3 program that makes primer selection possible.

Citing this site: "Candidate SSR marker primer pairs for this work were generated using the Zebrafish SSR search website, Massachusetts General Hospital, Charlestown MA 02129; World Wide Web URL: http://danio.mgh.harvard.edu/markers/ssr.html" (methods section).

Created and maintained by Iain Drummond,
Renal Unit, Massachusetts General Hospital

Last updated 5/10/2009