Content

Using Blast


     BLAST page provides an interface to BLAST algorithm to find sequence homology between a given sequence against sequences stored in SalmonDB. Also, is possible to change the subject database to other reference genome sequences from  species such as G. Aculeatus (Stickleback), T. Nigroviridis (green spotted puffer), O. Latipes (Medaka), T. Rubripes (Fugu) and Danio rerio (Zebrafish).


    The custom salmon EST databases are currently divided in protein sequences and nucleotide sequences for Rainbow trout and Atlantic salmon (Oncorhynchus mykiss and Salmo salar, respectively). To search, you shold use the apropiate BLAST program (blastp or blastx to query against protein databases and  blastn, tblastn or tblastx against nucleotide databases). Databases related to the others species mentioned above are also available as genomic, mRNA and protein sequences, according with their ENSEMBL annotation. Common parameters are also available for modification.


    Blast databases for the aquaculture species mentioned are also available as genomic, mRNA and protein sequence database according to ensembl annotation. The corresponding blast program must be used depending on the database selected (peptide sequence or DNA sequence).

Blast results are shown as depicted in the next figures.

    You can browse among relevant hits by clicking blue links under hit description (see red box in the figure). For Salmo salar and Oncorhynchus mykiss Gbrowse will display graphical information about the hit.

    For non-salmonid species, links redirects to corresponding ENSEMBL sequence website.