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.
This help document provides links to answers for the following questions:
What do I use the MouseBLAST form for?
Use this form to search mouse, rat, rodent, or human sequence database for sequences that may be associated with mouse genes. If a matching sequence is associated to an MGI mouse gene record, a detail report containing summary information and a link to MGI appears. You can either download the sequences for FASTA format matches or forward them to MouseBLAST for additional searches.
How do I use this form?
See Using MouseBLAST - Basic Steps.
How do I interpret the results of my search?
See Using MouseBLAST - Interpreting the MouseBLAST Output Report.
Are there any examples?
See Using MouseBLAST - Sample Queries.
What is BLAST? What is the difference between the WU-BLAST programs?
See Using MouseBLAST - Available BLAST Programs.
Which sequence databases can I search?
See Using MouseBLAST - Sequence Databases.
Are there different ways to mask a query sequence?
See Using MouseBLAST - Masking Programs.
Which sequence formats can I use on this form?
See Using MouseBLAST - Sequence Formats.
Can I find a sequence if I know the sequence accession ID?
See Using MouseBLAST - Searching By Sequence ID