This Help document answers questions about how to use the MGI MouseBLAST query form to search a sequence within mouse/rodent sequence databases to find matching sequences that may be associated with mouse genes. Query results may be linked to MGI mouse gene records. Searches are performed using WU-BLAST 2.0. All sequence databases are updated on a weekly basis. Basically, there are five actions:
Use MouseBLAST to search a sequence against a mouse, rat, rodent or human sequence database to find matching sequences. If a matching sequence is associated to an MGI mouse gene record, then summary information about that gene and a link to MGI is inserted in the output.
If any of the matching sequences are associated genes, the result is a display containing links to MGI mouse gene records. All matching sequences have links to the sequence provider's web site. See Search Results for details.
All six WU-BLAST 2.0 programs are available. Valid combinations of BLAST program with query sequence type, sequence database type, and alignment level are:
See Using MouseBLAST - Sequence Databases for a list of the searchable nucleotide and protein sequence databases.
There are several repeat masking programs you can run on your query sequence; these are especially useful when searching with genomic sequence. The following masking options are available.
There are four options for entering a query sequence. You can:
125618206 AND 125622026
125.618 AND 125.622
Number of scores to show Limits the number of matching sequences to appear in the summary list at the top of the BLAST results. Number of alignments to show Limits the number of matching sequence alignments to appear in the BLAST results.
For Search results, see Interpreting the MouseBLAST Output Report.Top