ZEBRAFISH and COMPARATIVE GENOMICS BLAST
This Blast server is maintained at the Massachusetts General Hospital Renal Unit by Iain Drummond and is hosted on a Sun Fire server, generously donated by Sun Microsystems.
This site has been updated (8/7/2009) to include Zebrafish genome assembly Zv8, finished and unfinished BACs.
Choose program to use and database to search:

Program Database

Enter sequence below in FASTA format

Or load it from disk

The query sequence is filtered for low complexity regions by default.
Filter Low complexity Mask for lookup table only

Expect    Matrix Perform ungapped alignment

Query Genetic Codes (blastx only)
Frame shift penalty for blastx

Other advanced options:     

Graphical Overview    Alignment view
Descriptions    Alignments Color schema

Other zebrafish links:

Generate candidate SSR markers in your own uploaded zebrafish DNA sequence.

Find candidate SSR markers in the Sanger zebrafish genome assemblies and sequenced BACs (8/7/2009).

The zebrafish assemblies can also be searched at the ensembl Danio rerio page at the Sanger Institute

ZFIN links to zebrafish genomic resources

Zon Lab database of zebrafish orthologs of human genes

Mouse resources:

Find candidate mouse SSR markers in NCBI build 35 genomic sequence.(4/2006)

Credits:

Sequence data for these databases is from the Sanger Center zebrafish genome sequencing project (whole genome shotgun sequence Sanger Center Conditions of Data Release ) and from the Washington University zebrafish EST project.

Blast web interface created by Sergei Shavirin