MGI's MouseBLAST will be retired in October 2015. BLAST queries will be forwarded to NCBI's BLAST server as follows:
- DNA queries will, by default, use the megablast program and will filter for rodent-specific repeats, though the first time you access the program the filtering options may be hidden. They should appear on subsequent visits.
- Protein queries will be forwarded to NCBI's Standard Protein BLAST with the blastp algorithm set by default.
- If you send SNP reference flanking sequence or gene trap sequence tags to NCBI BLAST, Mus musculus genomes will be searched by default.
- At NCBI's BLAST page you have the ability to alter the default settings.
The help document answers the following questions about the Forward to MouseBLAST form:
What's the purpose of this form?
Use this query form to search each sequence forwarded to MouseBLAST against a particular sequence database.
- MouseBLAST searches a forwarded sequence against a mouse, rat, rodent, or human sequence database to find matching sequences.
- The output of each search (sequences similar to the query sequence) appears in a separate web browser window.
- If a matching sequence is associated to an MGI mouse gene record, a summary of that gene and a link to MGI appear in the search results.
- You can download sequences for any matches in FASTA format or you can forward them to MouseBLAST for additional searching.
How do I use it?
For each sequence you want to search, do the following. Use the fields in the BLAST Program and Database column to specify MouseBLAST search options.
- Click/unclick the option to mask the query sequence. By default, the sequence is masked. For more information, see Using MouseBLAST - Masking Programs.
- Select the BLAST program to use. The default program is based on whether the query sequence is nucleotide or protein. For more information, see Using MouseBLAST - Available BLAST Programs.
- Select the sequence database to search. See Using MouseBLAST - Sequence Databases.
- Click Search. Results appear in a new browser window.
- Alternatively, you can search a sequence using the MouseBLAST Query Form by following the Advanced BLAST query form link.
How do I interpret the results?
The results of each search appear in a new web browser window. See Interpreting the MouseBLAST Output Report for details.
Are there any sample searches?
See Using MouseBLAST - Sample Queries.
Using the Forward to MouseBLAST Form