BLASTing against the growing body of mouse genomic data is easier than ever using the Mouse Genome BLAST page, which supports both untranslated and translated searches of a variety of mouse genome databases, including NCBI contigs and three draft assemblies of the genome.

The default database for Mouse Genome BLAST is the database of curated NCBI contigs, called “NT_Contigs”. These are assemblies of finished mouse BAC clones that are annotated with SNPs and STSs. Other databases include HTGS, Traces, BAC-Ends, Reference mRNAs and proteins from the NCBI RefSeq project, and ESTs.

The HTGS database is comprised of draft and finished sequence as submitted by the sequencing centers. The “Traces” database contains the mouse Whole Genome Shotgun (WGS) traces. The WGS Traces database may be searched with MegaBLAST, while the other databases may be queried with either nucleotide or protein sequences using the suite of blastn, blastp, tblastn, and blastx sequence-similarity search programs.

In addition, three assemblies of the mouse genome are available for searching. The first two, Phusion™ and Arachne, are preliminary assemblies of the mouse WGS reads based on a February data freeze and were created by the Sanger Center and the Whitehead Institute respectively. The third, the MGSCv3 assembly, produced by the Mouse Genome Sequencing Consortium, is comprised of WGS scaffolds generated using the end pairing information from the WGS reads. All three assemblies should be considered to be preliminary and will change as new data is added.

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