MGI 6.23 Using MouseBLAST

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?
How do I use this form?
How do I interpret the results of my search?
Are there any examples?
What is BLAST? What's the difference between the WU-BLAST programs?
Which sequence databases can I search?
What are the different ways to mask a query sequence?
Which sequence formats can I use on this form?
Can I find a sequence if I know the sequence accession ID?

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.

What do I use the MouseBLAST form for?

How do I use this form?

How do I interpret the results of my search?

Are there any examples?

What is BLAST? What is the difference between the WU-BLAST programs?

Which sequence databases can I search?

Are there different ways to mask a query sequence?

Which sequence formats can I use on this form?

Can I find a sequence if I know the sequence accession ID?